Adeno-associated viral vectors for treatment of niemann-pick disease type c

ABSTRACT

Provided herein are gene therapy compositions and methods for treating, preventing, and/or curing NPC1. More specifically, the disclosure provides Adeno-associated virus (AAV) vectors for delivery of nucleic acids and nucleic acids (including AAV transfer cassettes) for treating, preventing, and/or curing NPC1.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No.63/082,899, filed on Sep. 24, 2020, U.S. Provisional Application No.63/082,425, filed on Sep. 23, 2020, U.S. Provisional Application No.62/923,253, filed on Oct. 18, 2019, and U.S. Provisional Application No.62/916,749, filed on Oct. 17, 2019, each of which is incorporated byreference herein in its entirety.

DESCRIPTION OF THE TEXT FILE SUBMITTED ELECTRONICALLY

The contents of the text file submitted electronically herewith areincorporated by reference in their entirety: a computer readable formatcopy of the Sequence Listing (filename: STRD_021_02WO_SeqList_ST25.txt,date recorded Oct. 14, 2020, file size ˜425 kilobytes).

TECHNICAL FIELD

This application relates to recombinant adeno-associated virus (AAV)vectors. In some embodiments, the recombinant AAV vectors evadeneutralizing antibodies without decreased transduction efficiency.

BACKGROUND

Niemann-Pick Disease, type C1 (NPC1) is a neurodegenerative disordercharacterized by cholesterol accumulation in endolysosomal compartments.It is caused by mutations in the gene encoding NPC1, an endolysosomalprotein mediating intracellular cholesterol trafficking.

NPC1 can present in infants, children, or adults. Neonates can presentwith ascites and severe liver disease from infiltration of the liverand/or respiratory failure from infiltration of the lungs. Otherinfants, without liver or pulmonary disease, have hypotonia anddevelopmental delay. The classic presentation occurs in mid-to-latechildhood with the insidious onset of ataxia, vertical supranuclear gazepalsy (VSGP), and dementia. Dystonia and seizures are common. Dysarthriaand dysphagia eventually become disabling, making oral feedingimpossible; death usually occurs in the late second or third decade fromaspiration pneumonia. Adults are more likely to present with dementia orpsychiatric symptoms.

2-hydroxypropyl-β-cyclodextrin (HPBCD) has been shown to reduce thecholesterol and lipid accumulation and prolongs survival in NPC1 animalmodels. However, there are no therapies for NPC1 approved by the Foodand Drug Administration (FDA). Accordingly, there is an urgent need forcompositions and methods for treating, curing, and/or preventing NPC1.

BRIEF SUMMARY

Provided herein are gene therapy compositions and methods for treating,preventing, and/or curing NPC1. More specifically, the disclosureprovides Adeno-associated virus (AAV) vectors and nucleic acids(including nucleic acids comprising AAV transfer cassettes) fortreating, preventing, and/or curing NPC1.

In some embodiments, an adeno-associated virus (AAV) vector comprises:(i) a protein capsid comprising a capsid protein subunit comprising thesequence of SEQ ID NO: 180; and (ii) a nucleic acid encapsidated by theprotein capsid; wherein the nucleic acid comprises a transfer cassette;wherein the transfer cassette comprises, from 5′ to 3′: a 5′ invertedterminal repeat (ITR); a promoter; a transgene that encodes the NPC1protein; a polyadenylation signal; and a 3′ ITR.

In some embodiments, an adeno-associated virus (AAV) vector comprises:(i) a protein capsid comprising a capsid protein subunit comprising thesequence of SEQ ID NO: 180, or a sequence comprising about 1 to about 25amino acid mutations relative to SEQ ID NO: 180; and (ii) a nucleic acidencapsidated by the protein capsid; wherein the nucleic acid comprises atransfer cassette; wherein the transfer cassette comprises from 5′ to3′: a 5′ inverted terminal repeat (ITR); a promoter; a transgene whichencodes the NPC1 protein; a polyadenylation signal; and a 3′ ITR.

In some embodiments, the transfer cassette comprises an intronicsequence. In some embodiments, the intronic sequence comprises thesequence of SEQ ID NO: 10. In some embodiments, the intronic sequencemay be located between the promoter and the transgene.

In some embodiments, the 5′ ITR comprises the sequence of SEQ ID NO:3003.

In some embodiments, the 3′ ITR comprises the sequence of SEQ ID NO:3004.

In some embodiments, the promoter is the CBA promoter. In someembodiments, the promoter comprises the sequence of SEQ ID NO: 3005.

In some embodiments, the NPC1 protein is the human NPC1 protein. In someembodiments, the NPC1 protein comprises the sequence of SEQ ID NO: 3001.In some embodiments, the transgene comprises the sequence of SEQ ID NO:3002.

In some embodiments, the polyadenylation signal is the SV40polyadenylation signal. In some embodiments, the polyadenylation signalcomprises the sequence of SEQ ID NO: 3012.

In some embodiments, the transfer cassette comprises an enhancer.

In some embodiments, the transfer cassette comprises the sequence of SEQID NO: 3014. In some embodiments, the transfer cassette comprises thesequence of any one of SEQ ID NO: 3015-3019.

Also provided herein are compositions comprising an AAV vector of thedisclosure. Also provided herein are cells comprising an AAV vector ofthe disclosure.

Also provided here in are methods for treating a subject in need thereofcomprising administering to the subject an effective amount of an AAVvector, a nucleic acid, a composition, or a cell of the disclosure. Insome embodiments, the subject has Neimann-Pick Disease Type C. In someembodiments, the subject is a human subject

These and other embodiments are described in more detail below.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-1C. Bubble plots showing analysis of library diversity, directedevolution and enrichment of novel antigenic footprints. Parental (FIG.1A) and evolved libraries from a first round (FIG. 1B) and a secondround (FIG. 1C) of evolution were subjected to high-throughputsequencing using the Illumina MiSeq platform. Following analysis with acustom Perl script, enriched amino acid sequences were plotted. Eachbubble represents a distinct capsid protein subunit amino acid sequencewith the radius of the bubble proportional to the number of reads forthat variant in the respective library. The y-axis represents thepercentage of total reads from the sequencing run. Data are spread alongthe x-axis for ease of visualization. The percent reduction in uniqueclones (96.5%) directly demonstrates that numerous “un-fit” sequenceswere removed after a first and second round of evolution. Dominantisolates were selected for further analysis.

FIG. 2 . Volumetric yield of AAV vectors comprising protein capsidscomprising capsid protein subunit variants STRD.101 and STRD.102, ascompared to wildtype AAV9. Bars represent mean+/−95% confidenceinterval.

FIG. 3 . Infectivity values of AAV-STRD.101 and wildtype AAV9 determinedusing a standard TCID50 assay. Data are graphed as the natural log ofthe number of particles required to generate an infectious unit (P:IRatio). Error bars represent standard deviation.

FIG. 4A-4D. Transduction of U87 cells (FIG. 4A), N2A cells (FIG. 4B),Sy5Y cells (FIG. 4C), and U2OS cells (FIG. 4D) by recombinant AAVvectors comprising the STRD.101 capsid protein subunit and packaging aluciferase transgene, as compared to wildtype AAV9 vectors similarlypackaging a luciferase sequence. Error bars represent standard error.

FIG. 5 . Representative fluorescent microscopy images showing tdTomatoexpression in coronal vibratome sections 24 hours post-fixation with 4%PFA. Each section is 25 μm thick. Top panel shows images obtained usinga 4×objective lens with native tdTomato fluorescence. The bottom panelshows images obtained using a 10×objective lens with native tdTomatofluorescence.

FIG. 6 . Representative immunohistochemistry images showing tdTomatoexpression in coronal vibratome sections 24 hours post-fixation with 4%PFA. Each section is 25 μm thick.

FIG. 7 . Representative fluorescent microscopy images showing TdTomatoexpression in vibratrome liver sections 24 hours post-fixation with 4%PFA. Each section is 25 μm in thick. Panels show native tdTomatofluorescence with DAPI counterstain.

FIG. 8 . Representative fluorescent microscopy images showing TdTomatoexpression in vibratrome heart sections 24 hours post-fixation with 4%PFA. Each section is 50 μm in thick. Panels show native tdTomatofluorescence with DAPI counterstain.

FIG. 9 . Biodistribution of recombinant AAVs in non-human primates.Horizontal line shows limit of detection.

FIG. 10A is a graph that shows lysosomal phenotype, as determined bymeasuring LysoTracker® accumulation, in wildtype U2OS cells,NPC1-deficient (NPC1^(−/−)) U2OS cells, and NPC1^(−/−) cells transducedwith AAV2-hNPC at a Multiplicity of Infection (MOI) of either 5×10³ or10×10³. Statistical significance determined using one-way ANOVA. Errorbars represent standard error of the mean (SEM).

FIG. 10B is a graph that shows cholesterol accumulation, as determinedusing filipin staining, in wildtype U2OS cells, NPC1-deficient(NPC1^(−/−)) U2OS cells, and NPC1^(−/−) cells transduced with AAV2-hNPCat a Multiplicity of Infection (MOI) of either 5×10³ or 10×10³.Statistical significance determined using one-way ANOVA. Error barsrepresent SEM.

FIG. 11 is a Kaplan-Meier survival curve, showing survival of NPC1^(−/−)mice after retro-orbital injection with saline or with AAV9-hNPC1. AllAAV9-hNPC1-injected animals survived through the duration of theexperiment, and were sacrificed around 100 days of age for histologicalanalysis.

FIG. 12 shows behavioral phenotype score at about 10 weeks (70 days) ofage in wildtype mice, saline-treated NPC1^(−/−) mice, or NPC1^(−/−) miceinjected with AAV9-hNPC1. Statistical significance was determined usingan unpaired T-test, and error bars represent SEM.

FIG. 13 shows number of slips in a balance beam walking test at about 8weeks (56 days) of age in wildtype mice, saline-treated NPC1^(−/−) mice,or NPC1^(−/−) mice treated with AAV9-hNPC1. Error bars representstandard deviation.

DETAILED DESCRIPTION

Provided herein are recombinant AAV vectors which evade antibodyrecognition and/or selectively target tissues of the CNS. These AAVvectors may be useful for treating, preventing, and/or curing diseasessuch as NPC1.

AAVs are useful as gene delivery agents, and are powerful tools forhuman gene therapy. Using AAVs, high-frequency DNA delivery and stableexpression may be achieved in a variety of cells, both in vivo and invitro. Unlike some other viral vector systems, AAV does not requireactive cell division for stable integration in target cells.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this disclosure belongs. The terminology used in thedetailed description herein is for the purpose of describing particularembodiments only and is not intended to be limiting.

All publications, patent applications, patents, GenBank or otheraccession numbers and other references mentioned herein are incorporatedby reference in their entirety for all purposes.

The designation of amino acid positions in the AAV capsid proteinsubunits in the disclosure and the appended claims is with respect toVP1 numbering. It will be understood by those skilled in the art thatthe modifications described herein if inserted into the AAV cap gene mayresult in modifications in the VP1, VP2 and/or VP3 regions.Alternatively, the VP1, VP2, and/or VP3 can be expressed independentlyto achieve modification in only one or two of these regions (VP1, VP2,VP3, VP1+VP2, VP1+VP3, or VP2+VP3).

Definitions

The following terms are used in the description herein and the appendedclaims.

The singular forms “a,” “an” and “the” are intended to include theplural forms as well, unless the context clearly indicates otherwise.

Furthermore, the term “about” as used herein when referring to ameasurable value such as an amount of the length of a polynucleotide orpolypeptide sequence, dose, time, temperature, and the like, is meant toencompass variations of ±20%, 10%, 5%, 1%, ±0.5%, or even ±0.1% of thespecified amount.

Also as used herein, “and/or” refers to and encompasses any and allpossible combinations of one or more of the associated listed items, aswell as the lack of combinations when interpreted in the alternative(“or”).

Unless the context indicates otherwise, it is specifically intended thatthe various features described herein can be used in any combination.Moreover, in some embodiments, any feature or combination of featuresset forth herein can be excluded or omitted. To illustrate further, if,for example, the specification indicates that a particular amino acidcan be selected from A, G, I, L and/or V, this language also indicatesthat the amino acid can be selected from any subset of these aminoacid(s) for example A, G, I or L; A, G, I or V; A or G; only L; etc., asif each such subcombination is expressly set forth herein. Moreover,such language also indicates that one or more of the specified aminoacids can be disclaimed. For example, in some embodiments the amino acidis not A, G or I; is not A; is not G or V; etc., as if each suchpossible disclaimer is expressly set forth herein.

As used herein, the terms “reduce,” “reduces,” “reduction” and similarterms mean a decrease of at least about 10%, about 15%, about 20%, about25%, about 35%, about 50%, about 75%, about 80%, about 85%, about 90%,about 95%, about 97% or more.

As used herein, the terms “increase,” “improve,” “enhance,” “enhances,”“enhancement” and similar terms indicate an increase of at least about10%, about 15%, about 20%, about 25%, about 50%, about 75%, about 100%,about 150%, about 200%, about 300%, about 400%, about 500% or more.

The term “parvovirus” as used herein encompasses the familyParvoviridae, including autonomously replicating parvoviruses anddependoviruses. The autonomous parvoviruses include members of thegenera Protoparvovirus, Erythroparvovirus, Bocaparvovirus, andDensovirus subfamily. Exemplary autonomous parvoviruses include, but arenot limited to, minute virus of mouse, bovine parvovirus, canineparvovirus, chicken parvovirus, feline panleukopenia virus, felineparvovirus, goose parvovirus, H1 parvovirus, muscovy duck parvovirus,B19 virus, and any other autonomous parvovirus now known or laterdiscovered. Other autonomous parvoviruses are known to those skilled inthe art. See, e.g., BERNARD N. FIELDS et al, VIROLOGY, volume 2, chapter69 (4th ed., Lippincott-Raven Publishers; Cotmore et al. Archives ofVirology DOI 10.1007/s00705-013-1914-1).

As used herein, the term “adeno-associated virus” (AAV), includes but isnot limited to, AAV type 1, AAV type 2, AAV type 3 (including types 3Aand 3B), AAV type 4, AAV type 5, AAV type 6, AAV type 7, AAV type 8, AAVtype 9, AAV type 10, AAV type 11, AAV type 12, AAV type 13, AAV typerh32.33, AAV type rh8, AAV type rh10, AAV type rh74, AAV type hu.68,avian AAV, bovine AAV, canine AAV, equine AAV, ovine AAV, snake AAV,bearded dragon AAV, AAV2i8, AAV2g9, AAV-LK03, AAV7m8, AAV Anc80, AAVPHP.B, and any other AAV now known or later discovered. See, e.g.,BERNARD N. FIELDS et al., VIROLOGY, volume 2, chapter 69 (4th ed.,Lippincott-Raven Publishers). A number of AAV serotypes and clades havebeen identified (see, e.g., Gao et al, (2004) J. Virology 78:6381-6388;Moris et al, (2004) Virology 33-:375-383; and Table 2). Exemplary AAVcapsid protein subunit sequences for AAV1-9, AAVrh.10 and AAV11 areprovided in SEQ ID NO: 1-11.

As used herein, the term “chimeric AAV” refers to an AAV comprising aprotein capsid comprising capsid protein subunits with regions, domains,individual amino acids that are derived from two or more differentserotypes of AAV. In some embodiments, a chimeric AAV comprises a capsidprotein subunit comprised of a first region that is derived from a firstAAV serotype and a second region that is derived from a second AAVserotype. In some embodiments, a chimeric AAV comprises a capsid proteinsubunit comprised of a first region that is derived from a first AAVserotype, a second region that is derived from a second AAV serotype,and a third region that is derived from a third AAV serotype. In someembodiments, the chimeric AAV may comprise regions, domains, individualamino acids derived from AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8,AAV9, AAV10, AAV11, and/or AAV12. For example, the chimeric AAV mayinclude regions, domains, and/or individual amino acids from a first anda second AAV serotype as shown below (Table 1), wherein AAVX+Y indicatesa chimeric AAV including sequences derived from AAVX and AAVY:

TABLE 1 Chimeric AAVs Second AAV Serotype AAV1 AAV2 AAV3 AAV4 AAV5 AAV6AAV7 First AAV1 x AAV1 + 2 AAV1 + 3 AAV1 + 4 AAV1 + 5 AAV1 + 6 AAV1 + 7AAV AAV2 AAV2 + 1 x AAV2 + 3 AAV2 + 4 AAV2 + 5 AAV2 + 6 AAV2 + 7Sertoype AAV3 AAV3 + 1 AAV3 + 2 x AAV3 + 4 AAV3 + 5 AAV3 + 6 AAV3 + 7AAV4 AAV4 + 1 AAV4 + 2 AAV4 + 3 x AAV4 + 5 AAV4 + 6 AAV4 + 7 AAV5 AAV5 +1 AAV5 + 2 AAV5 + 3 AAV5 + 4 x AAV5 + 6 AAV5 + 7 AAV6 AAV6 + 1 AAV6 + 2AAV6 + 3 AAV6 + 4 AAV6 + 5 x AAV6 + 7 AAV7 AAV7 + 1 AAV7 + 2 AAV7 + 3AAV7 + 4 AAV7 + 5 AAV7 + 6 x AAV8 AAV8 + 1 AAV8 + 2 AAV8 + 3 AAV8 + 4AAV8 + 5 AAV8 + 6 AAV8 + 7 AAV9 AAV9 + 1 AAV9 + 2 AAV9 + 3 AAV9 + 4AAV9 + 5 AAV9 + 6 AAV9 + 7 AAV10 AAV10 + 1 AAV10 + 2 AAV10 + 3 AAV10 + 4AAV10 + 5 AAV10 + 6 AAV10 + 7 AAV11 AAV11 + 1 AAV11 + 2 AAV11 + 3AAV11 + 4 AAV11 + 5 AAV11 + 6 AAV11 + 7 AAV12 AAV12 + 1 AAV12 + 2AAV12 + 3 AAV12 + 4 AAV12 + 5 AAV12 + 6 AAV12 + 7 Second AAV SerotypeAAV8 AAV9 AAV10 AAV11 AAV12 First AAV1 AAV1 + 8 AAV1 + 9 AAV1 + 10AAV1 + 11 AAV1 + 12 AAV AAV2 AAV2 + 8 AAV2 + 9 AAV2 + 10 AAV2 + 11AAV2 + 12 Sertoype AAV3 AAV3 + 8 AAV3 + 9 AAV3 + 10 AAV3 + 11 AAV3 + 12AAV4 AAV4 + 8 AAV4 + 9 AAV4 + 10 AAV4 + 11 AAV4 + 12 AAV5 AAV5 + 8AAV5 + 9 AAV5 + 10 AAV5 + 11 AAV5 + 12 AAV6 AAV6 + 8 AAV6 + 9 AAV6 + 10AAV6 + 11 AAV6 + 12 AAV7 AAV7 + 8 AAV7 + 9 AAV7 + 10 AAV7 + 11 AAV7 + 12AAV8 x AAV8 + 9 AAV8 + 10 AAV8 + 11 AAV8 + 12 AAV9 AAV9 + 8 x AAV9 + 10AAV9 + 11 AAV9 + 12 AAV10 AAV10 + 8 AAV10 + 9 x AAV10 + 11 AAV10 + 12AAV11 AAV11 + 8 AAV11 + 9 AAV11 + 10 x AAV11 + 12 AAV12 AAV12 + 8AAV12 + 9 AAV12 + 10 AAV12 + 11 x

By including individual amino acids or regions from multiple AAVserotypes in one capsid protein subunit, capsid protein subunits thathave multiple desired properties that are separately derived from themultiple AAV serotypes may be obtained.

The genomic sequences of various serotypes of AAV and the autonomousparvoviruses, as well as the sequences of the native terminal repeats(TRs), Rep proteins, and capsid protein subunits are known in the art.Such sequences may be found in the literature or in public databasessuch as GenBank. See, e.g., GenBank Accession Numbers NC_002077,NC_001401, NC_001729, NC_001863, NC_001829, NC_001862, NC_000883,NC_001701, NC_001510, NC_006152, NC_006261, AF063497, U89790, AF043303,AF028705, AF028704, J02275, J01901, J02275, X01457, AF288061, AH009962,AY028226, AY028223, NC_001358, NC_001540, AF513851, AF513852, AY530579;the disclosures of which are incorporated by reference herein forteaching parvovirus and AAV nucleic acid and amino acid sequences. Seealso, e.g., Srivistava et al., (1983) J. Virology 45:555; Chiorini etal, (1998) J Virology 71:6823; Chiorini et al., (1999) J. Virology 73:1309; Bantel-Schaal et al., (1999) J Virology 73:939; Xiao et al, (1999)J Virology 73:3994; Muramatsu et al., (1996) Virology 221:208; Shade etal, (1986) J. Virol. 58:921; Gao et al, (2002) Proc. Nat. Acad. Sci. USA99:11854; Moris et al, (2004) Virology 33:375-383; international patentpublications WO 00/28061, WO 99/61601, WO 98/11244; and U.S. Pat. No.6,156,303; the disclosures of which are incorporated by reference hereinfor teaching parvovirus and AAV nucleic acid and amino acid sequences.See also Table 2. The protein capsid structures of autonomousparvoviruses and AAV are described in more detail in BERNARD N. FIELDSet al., VIROLOGY, volume 2, chapters 69 & 70 (4th ed., Lippincott-RavenPublishers). See also, description of the crystal structure of AAV2 (Xieet al., (2002) Proc. Nat. Acad. Sci. 99: 10405-10), AAV9 (DiMattia etal., (2012) J. Virol. 86:6947-6958), AAV8 (Nam et al, (2007) J. Virol.81: 12260-12271), AAV6 (Ng et al., (2010) J. Virol. 84:12945-12957),AAV5 (Govindasamy et al. (2013) J. Virol. 87, 11187-11199), AAV4(Govindasamy et al. (2006) J. Virol. 80:11556-11570), AAV3B (Lerch etal., (2010) Virology 403:26-36), BPV (Kailasan et al., (2015) J. Virol.89:2603-2614) and CPV (Xie et al, (1996) J. Mol. Biol. 6:497-520 andTsao et al, (1991) Science 251:1456-64).

TABLE 2 AAV Serotypes and Clades GenBank GenBank GenBank CompleteAccession Accession Accession Genomes Number Number Number Clade C Rh57AY530569 Adeno-associated NC_002077, Hu9 AY530629 Rh50 AY530563 virus 1AF063497 Adeno-associated NC_001401 Hu10 AY530576 Rh49 AY530562 virus 2Adeno-associated NC_001729 Hu11 AY530577 Hu39 AY530601 virus 3Adeno-associated NC_001863 Hu53 AY530615 Rh58 AY530570 virus 3BAdeno-associated NC_001829 Hu55 AY530617 Rh61 AY530572 virus 4Adeno-associated Y18065, Hu54 AY530616 Rh52 AY530565 virus 5 AF085716Adeno-associated NC_001862 Hu7 AY530628 Rh53 AY530566 virus 6 Avian AAVATCC AY186198, Hu18 AY530583 Rh51 AY530564 VR-865 AY629583, NC_004828Avian AAV strain NC_006263, Hu15 AY530580 Rh64 AY530574 DA-1 AY629583Bovine AAV NC_005889, Hu16 AY530581 Rh43 AY530560 AY388617, AAR26465AAV11 AAT46339, Hu25 AY530591 AAV8 AF513852 AY631966 AAV12 ABI16639,Hu60 AY530622 Rh8 AY242997 DQ813647 Clade A Ch5 AY243021 Rh1 AY530556AAV1 NC_002077, Hu3 AY530595 Clade F AF063497 AAV6 NC_001862 Hu1AY530575 Hu14 AY530579 (AAV9) Hu.48 AY530611 Hu4 AY530602 Hu31 AY530596Hu 43 AY530606 Hu2 AY530585 Hu32 AY530597 Hu 44 AY530607 Hu61 AY530623HSC1 MI332400.1 Hu 46 AY530609 Clade D HSC2 MI332401.1 Clade B Rh62AY530573 HSC3 MI332402.1 Hu. 19 AY530584 Rh48 AY530561 HSC4 MI332403.1Hu. 20 AY530586 Rh54 AY530567 HSC5 MI332405.1 Hu 23 AY530589 Rh55AY530568 HSC6 MI332404.1 Hu22 AY530588 Cy2 AY243020 HSC7 MI332407.1 Hu24AY530590 AAV7 AF513851 HSC8 MI332408.1 Hu21 AY530587 Rh35 AY243000 HSC9MI332409.1 Hu27 AY530592 Rh37 AY242998 HSC11 MI332406.1 Hu28 AY530593Rh36 AY242999 HSC12 MI332410.1 Hu 29 AY530594 Cy6 AY243016 HSC13MI332411.1 Hu63 AY530624 Cy4 AY243018 HSC14 MI332412.1 Hu64 AY530625 Cy3AY243019 HSC15 MI332413.1 Hu13 AY530578 Cy5 AY243017 HSC16 MI332414.1Hu56 AY530618 Rh13 AY243013 HSC17 MI332415.1 Hu57 AY530619 Clade E Hu68Hu49 AY530612 Rh38 AY530558 Clonal Isolate Hu58 AY530620 Hu66 AY530626AAV5 Y18065, AF085716 Hu34 AY530598 Hu42 AY530605 AAV 3 NC_001729 Hu35AY530599 Hu67 AY530627 AAV 3B NC_001863 AAV2 NC_001401 Hu40 AY530603AAV4 NC_001829 Hu45 AY530608 Hu41 AY530604 Rh34 AY243001 Hu47 AY530610Hu37 AY530600 Rh33 AY243002 Hu51 AY530613 Rh40 AY530559 Rh32 AY243003Hu52 AY530614 Rh2 AY243007 Others Hu T41 AY695378 Bb1 AY243023 Rh74 HuS17 AY695376 Bb2 AY243022 Bearded Dragon AAV Hu T88 AY695375 Rh10AY243015 Snake NC_006148.1 AAV Hu T71 AY695374 Hu17 AY530582 Hu T70AY695373 Hu6 AY530621 Hu T40 AY695372 Rh25 AY530557 Hu T32 AY695371 Pi2AY530554 Hu T17 AY695370 Pi1 AY530553 Hu LG15 AY695377 Pi3 AY530555

Recombinant AAV (rAAV) vectors can be produced in culture using viralproduction cell lines. The terms “viral production cell”, “viralproduction cell line,” or “viral producer cell” refer to cells used toproduce viral vectors. HEK293 and 239T cells are common viral productioncell lines. Table 3, below, lists exemplary viral production cell linesfor various viral vectors. Production of rAAVs typically requires thepresence of three elements in the cells: 1) a transgene flanked by AAVinverted terminal repeat (ITR) sequences, 2) AAV rep and cap genes, and3) helper virus protein sequences. These three elements may be providedon one or more plasmids, and transfected or transduced into the cells.

TABLE 3 Exemplary viral production cell lines Exemplary Viral VirusVector Production Cell Line(s) Adenovirus HEK293, 911, pTG6559, PER.C6,GH329, N52.E6, HeLa-E1, UR, VLI-293 Adeno-Associated Virus HEK293, Sf9(AAV) Retrovirus HEK293 Lentivirus 293T

“HEK293” refers to a cell line originally derived from human embryonickidney cells grown in tissue culture. The HEK293 cell line grows readilyin culture, and is commonly used for viral production. As used herein,“HEK293” may also refer to one or more variant HEK293 cell lines, i.e.,cell lines derived from the original HEK293 cell line that additionallycomprise one or more genetic alterations. Many variant HEK293 lines havebeen developed and optimized for one or more particular applications.For example, the 293T cell line contains the SV40 large T-antigen thatallows for episomal replication of transfected plasmids containing theSV40 origin of replication, leading to increased expression of desiredgene products.

“Sf9” refers to an insect cell line that is a clonal isolate derivedfrom the parental Spodoptera frugiperda cell line IPLB-Sf-21-AE. Sf9cells can be grown in the absence of serum and can be cultured attachedor in suspension.

A “transfection reagent” means a composition that enhances the transferof nucleic acid into cells. Some transfection reagents commonly used inthe art include one or more lipids that bind to nucleic acids and to thecell surface (e.g., Lipofectamine™)

As used herein, the term “multiplicity of infection” or “MOI” refers tonumber of virions contacted with a cell. For example, cultured cells maybe contacted with AAVs at an MOI in the range of 1×10² to 1×10⁵ virionsper cell.

The term “self-complimentary AAV” or “scAAV” refers to a recombinant AAVvector comprising a nucleic acid (i.e., a DNA) which forms a dimericinverted repeat molecule that spontaneously anneals, resulting inearlier and more robust transgene expression compared with conventionalsingle-strand (ss) AAV genomes. See, e.g., McCarty, D. M., et al., GeneTherapy 8, 1248-1254 (2001). Unlike conventional ssAAV, scAAV can bypasssecond-strand synthesis, the rate-limiting step for gene expression.Moreover, double-stranded scAAV is less prone to DNA degradation afterviral transduction, thereby increasing the number of copies of stableepisomes. Notably, scAAV can typically only hold a genome that is about2.4 kb, half the size of a conventional AAV vector. In some embodiments,the AAV vectors described herein are self-complementary AAVs.

As used herein, the term “peptide” refers to a short amino acidsequence. The term peptide may be used to refer to portion or region ofan AAV capsid protein subunit amino acid sequence. The peptide may be apeptide that naturally occurs in a native AAV capsid protein, or apeptide that does not naturally occur in a native AAV capsid protein.Naturally occurring AAV peptides in an AAV capsid protein may besubstituted by non-naturally occurring peptides. For example, anon-naturally occurring peptide may be substituted into an AAV capsidprotein to provide a modified capsid protein, such that thenaturally-occurring peptide is replaced by the non-naturally occurringpeptide.

The term “tropism” as used herein refers to preferential entry of thevirus into certain cells or tissues, optionally followed by expression(e.g., transcription and, optionally, translation) of a sequence(s)carried by the viral genome in the cell, e.g., for a recombinant virus,expression of a transgene of interest.

As used here, “systemic tropism” and “systemic transduction” (andequivalent terms) indicate that the virus vector or a virus-likeparticle as described herein exhibits tropism for or transduces,respectively, tissues throughout the body (e.g., brain, lung, skeletalmuscle, heart, liver, kidney and/or pancreas). In some embodiments,systemic transduction of muscle tissues (e.g., skeletal muscle,diaphragm and cardiac muscle) is achieved. In some embodiments, systemictransduction of skeletal muscle tissues is achieved. For example, insome embodiments, essentially all skeletal muscles throughout the bodyare transduced (although the efficiency of transduction may vary bymuscle type). In some embodiments, systemic transduction of limbmuscles, cardiac muscle and diaphragm muscle is achieved. Optionally,the virus vector or virus-like particle is administered via a systemicroute (e.g., systemic route such as intravenously, intra-articularly orintra-lymphatically).

Alternatively, in some embodiments, the virus vector or virus-likeparticle is delivered locally (e.g., to the footpad, intramuscularly,intradermally, subcutaneously, topically). In some embodiments, thevirus vector or virus-like particle is delivered locally to a tissue ofthe central nervous system (CNS), such as the brain or the spinal cord.In some embodiments, the virus vector or virus-like particle isadministered by intrathecal, intracerebral or intracerebroventricularinjection.

Unless indicated otherwise, “efficient transduction” or “efficienttropism,” or similar terms, can be determined by reference to a suitablecontrol (e.g., at least about 50%, about 60%, about 70%, about 80%,about 85%, about 90%, about 95% or more of the transduction or tropism,respectively, of the control). In some embodiments, the virus vector(e.g., the AVV vector) efficiently transduces or has efficient tropismfor skeletal muscle, cardiac muscle, diaphragm muscle, pancreas(including p-islet cells), spleen, the gastrointestinal tract (e.g.,epithelium and/or smooth muscle), cells of the central nervous system,lung, joint cells, and/or kidney. Suitable controls will depend on avariety of factors including the desired tropism profile. For example,AAV8 and AAV9 are highly efficient in transducing skeletal muscle,cardiac muscle and diaphragm muscle, but have the disadvantage of alsotransducing liver with high efficiency. Thus, viral vectors can beidentified that demonstrate the efficient transduction of skeletal,cardiac and/or diaphragm muscle of AAV8 or AAV9, but with a much lowertransduction efficiency for liver. Further, because the tropism profileof interest may reflect tropism toward multiple target tissues, it willbe appreciated that a suitable virus vector may represent sometradeoffs. To illustrate, a virus vector may be less efficient than AAV8or AAV9 in transducing skeletal muscle, cardiac muscle and/or diaphragmmuscle, but because of low level transduction of liver, may nonethelessbe very desirable.

Similarly, it can be determined if a virus “does not efficientlytransduce” or “does not have efficient tropism” for a target tissue, orsimilar terms, by reference to a suitable control. In some embodiments,the virus vector does not efficiently transduce (i.e., does not haveefficient tropism) for liver, kidney, gonads and/or germ cells. In someembodiments, undesirable transduction of tissue(s) (e.g., liver) isabout 20% or less, about 10% or less, about 5% or less, about 1% orless, about 0.1% or less of the level of transduction of the desiredtarget tissue(s) (e.g., skeletal muscle, diaphragm muscle, cardiacmuscle and/or cells of the central nervous system).

As used herein in connection with an AAV vector (or a protein capsid,capsid protein subunit, or peptide thereof), the terms “selectivelybinds,” “selective binding” and similar terms, refer to binding of theAAV vector (or a protein capsid, capsid protein subunit, or peptidethereof) to a target in a manner dependent upon the presence of aparticular molecular structure. In some embodiments, selective bindingrefers to binding of the AAV predominantly to a specific target, withoutsubstantial or significant binding to other targets. In someembodiments, an AAV vector (or a protein capsid, capsid protein subunit,or peptide thereof) specifically binds to a receptor in a cell or tissueof interest, but does not exhibit substantial or significant binding toother receptors.

A “polynucleotide” is a sequence of nucleotide bases, and may be RNA,DNA or DNA-RNA hybrid sequences (including both naturally occurring andnon-naturally occurring nucleotide). In some embodiments, apolynucleotide is either a single or double stranded DNA sequence.

As used herein, an “isolated” polynucleotide (e.g., an “isolated DNA” oran “isolated RNA”) means a polynucleotide at least partially separatedfrom at least some of the other components of the naturally occurringorganism or virus, for example, the cell or viral structural componentsor other polypeptides or nucleic acids commonly found associated withthe polynucleotide. In some embodiments an “isolated” nucleotide isenriched by at least about 10-fold, about 100-fold, about 1000-fold,about 10,000-fold or more as compared with the starting material.

Likewise, an “isolated” polypeptide means a polypeptide that is at leastpartially separated from at least some of the other components of thenaturally occurring organism or virus, for example, the cell or viralstructural components or other polypeptides or nucleic acids commonlyfound associated with the polypeptide. In some embodiments an “isolated”polypeptide is enriched by at least about 10-fold, about 100-fold, about1000-fold, about 10,000-fold or more as compared with the startingmaterial.

As used herein, by “isolate” or “purify” (or grammatical equivalents) avirus vector, it is meant that the virus vector is at least partiallyseparated from at least some of the other components in the startingmaterial. In some embodiments an “isolated” or “purified” virus vectoris enriched by at least about 10-fold, about 100-fold, about 1000-fold,about 10,000-fold or more as compared with the starting material.

A “therapeutic” polypeptide or protein is one that can alleviate,reduce, prevent, delay and/or stabilize symptoms that result from anabsence or defect in a protein in a cell or subject and/or is apolypeptide that otherwise confers a benefit to a subject, e.g.,anti-cancer effects or improvement in transplant survivability.

By the terms “treat,” “treating” or “treatment of” (and grammaticalvariations thereof) it is meant that the severity of the subject'scondition is reduced, at least partially improved or stabilized and/orthat some alleviation, mitigation, decrease or stabilization in at leastone clinical symptom is achieved and/or there is a delay in theprogression of the disease or disorder.

The terms “prevent,” “preventing” and “prevention” (and grammaticalvariations thereof) refer to prevention and/or delay of the onset of adisease, disorder and/or a clinical symptom(s) in a subject and/or areduction in the severity of the onset of the disease, disorder and/orclinical symptom(s) relative to what would occur in the absence of thecompositions and/or methods described herein. The prevention can becomplete, e.g., the total absence of the disease, disorder and/orclinical symptom(s). The prevention can also be partial, such that theoccurrence of the disease, disorder and/or clinical symptom(s) in thesubject and/or the severity of onset is less than what would occur inthe absence of the compositions and/or methods described herein.

As used herein, an “effective amount” is the amount of an AAV vector,nucleic acid, or other agent provided herein that is effective to treator prevent a disease or disorder in a subject or to ameliorate a sign orsymptom thereof. The “effective amount” may vary depending, for example,on the disease and/or symptoms of the disease, severity of the diseaseand/or symptoms of the disease or disorder, the age, weight, and/orhealth of the patient to be treated, and the judgment of the prescribingphysician. An appropriate amount in any given instance may beascertained by those skilled in the art or may be capable ofdetermination by routine experimentation.

As used herein, the terms “virus vector,” “vector” refer to a virus(e.g., AAV) particle that functions as a nucleic acid delivery vehicle,and which comprises a vector genome (e.g., a nucleic acid comprising atransgene) packaged within a virion or virus-like particle.

An “adeno-associated virus vector” or “AAV vector” typically comprises aprotein capsid, and a nucleic acid (e.g., a nucleic acid comprising atransgene) encapsidated by the protein capsid. The “protein capsid” is anear-spherical protein shell that comprises individual “capsid proteinsubunits” (e.g., about 60 capsid protein subunits) associated andarranged with T=1 icosahedral symmetry. The protein capsids of the AAVvectors described herein comprise a plurality of capsid proteinsubunits. When an AAV vector is described as comprising an AAV capsidprotein subunit, it will be understood that the AAV vector comprises aprotein capsid, wherein the protein capsid comprises one or more AAVcapsid protein subunits. As used herein, the term “capsid protein” issometimes used to refer to a capsid protein subunit. The term“viral-like particle” or “virus-like particle” refers to a proteincapsid that does not comprise any vector genome or nucleic acidcomprising a transfer cassette or transgene.

In some embodiments, an AAV vector may comprise a nucleic acidcomprising a “transfer cassette,” i.e., a nucleic acid comprising one ormore sequences which can be delivered by the AAV to a cell. In someembodiments, the nucleic acid is self-complementary (i.e., doublestranded). In some embodiments, the nucleic acid is notself-complimentary (i.e., single stranded).

A “rAAV vector genome” or “rAAV genome” is an AAV genome (i.e., vDNA)that comprises one or more heterologous nucleic acid sequences. rAAVvectors generally require only the inverted terminal repeat(s) (ITR(s))in cis to promote nucleic acid replication. All other viral sequencesare dispensable and may be supplied in trans (Muzyczka, (1992) Curr.Topics Microbiol. Immunol. 158:97). Typically, the rAAV vector genomewill only retain the one or two ITR sequences so as to maximize the sizeof the transgene that can be efficiently packaged by the AAV vector. Thestructural and non-structural protein coding sequences may be providedin trans (e.g., from a a plasmid, or by stably integrating the sequencesinto a packaging cell). In some embodiments, the rAAV vector genomecomprises at least one ITR sequence (e.g., AAV ITR sequence), optionallytwo ITRs (e.g., two AAV ITRs), which typically will be at the 5′ and 3′ends of the vector genome (i.e., the 5′ ITR and the 3′ ITR) and flankthe heterologous nucleic acid, but need not be contiguous thereto.

The virus vectors described herein can further be “targeted” virusvectors (e.g., having a directed tropism) and/or “hybrid” virus vectors(i.e., in which the viral ITRs and viral protein capsid are fromdifferent viruses) as described in international patent publicationWO00/28004 and Chao et al, (2000) Molecular Therapy 2:619. In someembodiments, the virus vectors are targeted to a cell and/or tissue ofthe CNS.

The virus vectors described herein can further be duplexed virusparticles as described in international patent publication WO 01/92551(the disclosure of which is incorporated herein by reference in itsentirety). Thus, in some embodiments, double stranded (duplex) genomescan be packaged into the virus protein capsids described herein.Further, the protein capsid, protein capsid subunits, or genomicelements can contain other modifications, including insertions,deletions and/or substitutions.

As used herein, the term “amino acid” encompasses any naturallyoccurring amino acid, modified forms thereof, and synthetic amino acids.Naturally occurring, levorotatory (L-) amino acids are shown in Table 4.

TABLE 4 Amino acid residues and abbreviations. Abbreviation Amino AcidResidue Three-Letter Code One-Letter Code Alanine Ala A Arginine Arg RAsparagine Asn N Aspartic acid (Aspartate) Asp D Cysteine Cys CGlutamine Gln Q Glutamic acid (Glutamate) Glu E Glycine Gly G HistidineHis H Isoleucine Ile I Leucine Leu L Lysine Lys K Methionine Met MPhenylalanine Phe F Proline Pro P Serine Ser S Threonine Thr TTryptophan Trp W Tyrosine Tyr Y Valine Val V

Alternatively, the amino acid can be a modified amino acid residue(nonlimiting examples are shown in Table 5) and/or can be an amino acidthat is modified by post-translation modification (e.g., acetylation,amidation, formylation, hydroxylation, methylation, phosphorylation orsulfatation). Methods of chemically modifying amino acids are known inthe art (see, e.g., Greg T. Hermanson, Bioconjugate Techniques, 1^(st)edition, Academic Press, 1996).

TABLE 5 Modified Amino Acid Residues Modified Amino Acid ResidueAbbreviation Amino Acid Residue Derivatives 2-Aminoadipic acid Aad3-Aminoadipic acid bAad beta-Alanine, beta-Aminoproprionic acid bAla2-Aminobutyric acid Abu 4-Aminobutyric acid, Piperidinic acid 4Abu6-Aminocaproic acid Acp 2-Aminoheptanoic acid Ahe 2-Aminoisobutyric acidAib 3-Aminoisobutyric acid bAib 2-Aminopimelic acid Apm t-butylalaninet-BuA Citrulline Cit Cyclohexylalanine Cha 2,4-Diaminobutyric acid DbuDesmosine Des 2,21-Diaminopimelic acid Dpm 2,3-Diaminoproprionic acidDpr N-Ethylglycine EtGly N-Ethylasparagine EtAsn Homoarginine hArgHomocysteine hCys Homoserine hSer Hydroxylysine Hyl Allo-HydroxylysineaHyl 3-Hydroxyproline 3Hyp 4-Hydroxyproline 4Hyp Isodesmosine Ideallo-Isoleucine alle Methionine sulfoxide MSO N-Methylglycine, sarcosineMeGly N-Methyl isoleucine Melle 6-N-Methyllysine MeLys N-MethylvalineMeVal 2-Naphthylalanine 2-Nal Norvaline Nva Norleucine Nle Ornithine Orn4-Chlorophenylalanine Phe(4-C1) 2-Fluorophenylalanine Phe(2-F)3-Fluorophenylalanine Phe(3-F) 4-Fluorophenylalanine Phe(4-F)Phenylglycine Phg Beta-2-thienylalanine Thi

Further, the non-naturally occurring amino acid can be an “unnatural”amino acid (as described by Wang et al., Annu Rev Biophys Biomol Struct.35-225-49 (2006)). These unnatural amino acids can advantageously beused to chemically link molecules of interest to the AAV protein capsidor capsid protein subunit.

Modified AAV Protein Capsid Subunits, Protein Capsids, and AAV VectorsComprising the Same AAV Vectors

Additionally provided herein are adeno-associated virus (AAV) vectorscomprising (i) a protein capsid comprising recombinant capsid proteinsubunits and (ii) a transfer cassette encapsidated by the proteincapsid. In some embodiments, the recombinant capsid protein subunits(including VP1, VP2 and/or VP3 regions) may comprise a peptide in theiramino acid sequence that does not occur in any native AAV capsid proteinsubunit sequence. Capsid protein subunits comprising the peptidesdescribed herein can confer one or more desirable properties to virusvectors including, without limitation, the ability to evade neutralizingantibodies. Thus, AAV vectors described herein address the limitationsassociated with conventional AAV vectors.

Accordingly, in some embodiments, the present disclosure providesadeno-associated virus (AAV) vectors comprising (i) one or morerecombinant capsid proteins and (ii) a transfer cassette encapsidated bythe protein capsid; wherein the capsid protein comprises a peptidehaving the sequence of any one of SEQ ID NO: 12-20. In some embodiments,the transfer cassette comprises 5′ and 3′ AAV inverted terminal repeats.In some embodiments, the transfer cassette comprises a transgene (e.g.,a NPC1 transgene). In some embodiments, the transfer cassette is doublestranded. In some embodiments, the transfer cassette is single stranded.In some embodiments, the transgene encodes a therapeutic protein or RNA.In some embodiments, the recombinant capsid protein has at least 90%, atleast 95%, at least 96%, at least 97%, at least 98%, or at least 99%sequence identity to the native sequence of the AAV1, AAV2, AAV3, AAV4,AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, AAVrh.8, AAVrh.10,AAVrh32.33, AAVrh74, bovine AAV or avian AAV capsid protein. In someembodiments, the recombinant capsid protein has at least 90% sequenceidentity to the native sequence of the AAV9 capsid protein.

In some embodiments, the peptide is located at the amino acid positionscorresponding to amino acids 451-458 of the native AAV9 capsid proteinsubunit, or the equivalent amino acid residues in AAV1, AAV2, AAV3,AAV4, AAV5, AAV6, AAV7, AAV8, AAV10, AAV11, AAV12, AAVrh.8, AAVrh.10,AAVrh32.33, AAVrh74, bovine AAV or avian AAV, and the peptide isselected from any one of SEQ ID NO: 12-18. In some embodiments, thepeptide is located at the amino acid positions corresponding to aminoacids 587-594 of the native AAV9 capsid protein subunit, or theequivalent amino acid residues in AAV1, AAV2, AAV3, AAV4, AAV5, AAV6,AAV7, AAV8, AAV10, AAV11, AAV12, AAVrh.8, AAVrh.10, AAVrh32.33, AAVrh74,bovine AAV or avian AAV, and the peptide is selected from SEQ ID NO: 19or 20.

In some embodiments, a recombinant capsid protein subunit comprises a) afirst peptide having a sequence of any one of SEQ ID NO: 12-18; and b) asecond peptide having a sequence of any one of SEQ ID NO: 19-20. In someembodiments, the first peptide is at amino acid positions 451-458, andthe second peptide is at amino acids 587-594, wherein the amino acidnumbering is based on the native AAV9 capsid protein subunit, or theequivalent amino acid residues in AAV1, AAV2, AAV3, AAV4, AAV5, AAV6,AAV7, AAV8, AAV10, AAV11, AAV12, AAVrh.8, AAVrh.10, AAVrh32.33, AAVrh74,bovine AAV or avian AAV.

In some embodiments, the peptide inhibits binding of at least oneantibody to the protein capsid or a capsid protein subunit thereof. Insome embodiments, the peptide inhibits neutralization of infectivity ofthe AAV vector by the antibody.

In some embodiments, the peptide selectively binds to a receptorexpressed on the surface of a cell in the central nervous system (CNS).In some embodiments, the cell is in the premotor cortex, the thalamus,the cerebellar cortex, the dentate nucleus, the spinal cord, or thedorsal root ganglion. In some embodiments, the peptide selectively bindsto a receptor expressed on the surface of a cell in the heart.

In some embodiments, an adeno-associated virus (AAV) vector comprises(i) a protein capsid comprising a mutant AAV9 capsid protein subunit and(ii) a transfer cassette encapsidated by the protein capsid, wherein thecapsid protein subunit comprises a peptide having the sequenceX¹-X²-X³-X⁴-X⁵-X⁶-X⁷-X⁸ (SEQ ID NO: 158) at amino acids 451-458 of thenative AAV9 capsid protein subunit sequence, wherein the peptide doesnot occur in the native AAV9 capsid protein subunit sequence. In someembodiments, X¹ is not I, X² is not N, X³ is not G, X⁴ is not S, X⁵ isnot G, X⁶ is not Q, X⁷ is not N, and/or X⁸ is not Q. In someembodiments, X¹ is S, F, Q, G, K, or R. In some embodiments, X² is C, G,R, D, T, or Q. In some embodiments, X³ is Q, V, G, Y, R, F, or D. Insome embodiments, X⁴ is P, Q, A, or R. In some embodiments, X⁵ is T, N,A, P, or I. In some embodiments, X⁶ is V, Q, A, or I. In someembodiments, X⁷ is M, P, R, Q, or N. In some embodiments, X⁸ is N, L, F,E, H, or A. In some embodiments, X¹ is S, X² is C, X³ is Q, X⁴ is P, X⁵is T, X⁶ is V, X⁷ is M, and X⁸ is N. In some embodiments, X¹ is F, X² isG, X³ is V, X⁴ is P, X⁵ is N, X⁶ is Q, X⁷ is P, and X⁸ is L. In someembodiments, X¹ is Q, X² is R, X³ is G, X⁴ is Q, X⁵ is A, X⁶ is A, X⁷ isP, and X⁸ is F. In some embodiments, X¹ is G, X² is D, X³ is Y, X⁴ is A,X⁵ is P, X⁶ is I, X⁷ is R, and X⁸ is E. In some embodiments, X¹ is K, X²is T, X³ is R, X⁴ is R, X⁵ is I, X⁶ is V, X⁷ is Q, and X⁸ is H. In someembodiments, X¹ is F, X² is G, X³ is F, X⁴ is P, X⁵ is N, X⁶ is Q, X⁷ isP, and X⁸ is L. In some embodiments, X¹ is R, X² is Q, X³ is D, X⁴ is Q,X⁵ is P, X⁶ is I, X⁷ is N, and X⁸ is A.

In some embodiments, an adeno-associated virus (AAV) vector comprises(i) a protein capsid comprising a mutant AAV9 capsid protein subunit and(ii) a transfer cassette encapsidated by the protein capsid, wherein thecapsid protein subunit comprises a peptide having the sequenceX¹-X²-X³-X⁴-X⁵-X⁶-X⁷-X⁸ (SEQ ID NO: 158) at amino acids 587-594 of thenative AAV9 capsid protein subunit sequence, wherein the peptide doesnot occur in the native AAV9 capsid protein subunit sequence. In someembodiments, X¹ is not A, X² is not Q, X³ is not A, X⁴ is not Q, X⁵ isnot A, X⁶ is not Q, X⁷ is not T, and/or X⁸ is not G. In someembodiments, X¹ is S. In some embodiments, X² is K or T. In someembodiments, X³ is V. In some embodiments, X⁴ is E or D. In someembodiments, X⁵ is S. In some embodiments, X⁶ is W or I. In someembodiments, X⁷ is T or A. In some embodiments, X⁸ is E or I. In someembodiments, X¹ is S, X² is K, X³ is V, X⁴ is E, X⁵ is S, X⁶ is W, X⁷ isT, and X⁸ is E. In some embodiments, X¹ is S, X² is T, X³ is V, X⁴ is D,X⁵ is S, X⁶ is I, X⁷ is A, and X⁸ is I.

In some embodiments, an adeno-associated virus (AAV) vector comprises(i) a protein capsid comprising a recombinant capsid protein subunit and(ii) a transfer cassette encapsidated by the protein capsid, wherein thecapsid protein subunit comprises an amino acid sequence that is at least95%, at least 96%, at least 97%, at least 98%, or at least 99% identicalto any one of SEQ ID NO: 165-187. In some embodiments, the capsidprotein subunit comprises the amino acid sequence of any one of SEQ IDNO: 165-187. In some embodiments, the capsid protein subunit comprisesthe amino acid sequence of SEQ ID NO: 175. In some embodiments, thecapsid protein subunit comprises the amino acid sequence of SEQ ID NO:180.

In some embodiments, an AAV vector selectively delivers the transfercassette to a cell or tissue of the central nervous system. In someembodiments, the tissue of the central nervous system is the premotorcortex, the thalamus, the cerebellar cortex, the dentate nucleus, thespinal cord, or the dorsal root ganglion. In some embodiments, the AAVvector delivers the transfer cassette to the brain, but does not deliverthe AAV vector to the heart. In some embodiments, the AAV vectordelivers the transfer cassette to the brain and to the heart. In someembodiments, delivery of the transfer cassette is greater to the brainthan to the heart. In some embodiments, delivery of the transfercassette is approximately equal in the brain and in the heart.

AAV Capsid Protein Subunits and Protein Capsids Comprising the Same

In some embodiments, the disclosure provides an adeno-associated virus(AAV) capsid protein subunit comprising one or more amino acidmodifications (e.g., substitutions and/or deletions) compared to anative AAV capsid protein subunit, wherein the one or more modificationsmodify one or more antigenic sites on the AAV capsid protein subunit.The modification of the one or more antigenic sites results in reducedrecognition by an antibody of the one or more antigenic sites and/orinhibition of neutralization of infectivity of a virus particlecomprising the AAV capsid protein subunit. The one or more amino acidmodifications (e.g., substitutions and/or deletions) can be in one ormore antigenic footprints identified by peptide epitope mapping and/orcryo-electron microscopy studies of AAV-antibody complexes containingAAV capsid protein subunits. In some embodiments, the one or moreantigenic sites are common antigenic motifs or CAMs as described in WO2017/058892, which is incorporated herein by reference in its entirety.In some embodiments, the antigenic sites are in a variable region (VR)of the AAV capsid protein subunit, such as VR-I, VR-II, VR-III, VR-IV,VR-V, VR-VI, VR-VII, VR-VIII, VR-IX. In some embodiments, one or moreantigenic sites is in the HI loop of the AAV capsid protein subunit.

In some embodiments, an AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8,AAV9, AAVrh8, AAVrh10, AAV10, AAV11, AAV12, AAVrh32.22, bovine AAV, orAvian AAV capsid protein subunit comprises an amino acid modification(e.g., a substitution or deletion) in one or more of the regionsidentified in Table 6, below.

TABLE 6 Exemplary antigenic or other regions on various AAV capsid   protein subunits that may be partially or fully substituted/ replaced. Respective VP1 numbering of residues in the native AAV capsid protein subunit sequence is shown. AAV1 AAV2 AAV3AAV4 AAV5 Sequence Sequence Sequence Sequence Sequence (amino SEQ (aminoSEQ (amino SEQ (amino SEQ (amino SEQ acid ID acid ID acid ID acid IDacid ID numbers) NO numbers) NO numbers) NO numbers) NO numbers) NOSASTGAS 2591 SQSGAS 2601 SQSGAS 2611 RLGESL 2621 EIKSGSVD 2631 (262-268)(262-267) (262-267) QS GS (253-260) (249-258) VFMIPQY 2592 VFMVPQY 2602VFMVPQ 2612 VFMVPQ 2622 VFTLPQY 2632 GYL GYL YGYL YGYC GYA (370-379)(369-378) (369-378) (360-369) (360-369) NQSGSA 2593 TPSGTTT 2603 TTSGTTN2613 GTTLNA 2623 STNNTGG 2633 QNK QS QS GTA VQ (451-459) (450-458)(451-459) (445-453) (440-448) SV 2594 RD 2604 SL 2614 SN 2624 AN 2634(472-473) (471-472) (472-473) (466-467) (458-459) KTDNNN 2595 SADNNNS2605 ANDNNN 2615 ANQNYKI 2625 SGVNRAS 2635 SN E SN PATGS (479-485)(493-500) (492-499) (493-500) (487-498) KDDEDK 2596 KDDEEKF 2606 KDDEEK2616 GPADSK 2626 LQGSNTY 2636 F (527-533) F F (515-521) (528-534)(528-534) (527-533) SAGASN 2597 GSEKTN 2607 GTTASN 2617 QNGNTA 2627ANPGTTA 2637 (547-552) (546-551) (547-552) (545-560) T (534-541) STDPATG2598 NRQAATA 2608 NTAPTTG 2618 SNLPTV 2628 TTAPATG 2638 DVH DVN TVN DRLTTYN (588-597) (587-596) (588-597) (583-595) (577-586) AN 2599 VN 2609 VN2619 NS 2629 QF 2639 (709-710) (708-709) (709-710) (707-708) (697-698)DNNGLY 2600 DTNGVYS 2610 DTNGVY 2620 DAAGKY 2630 DSTGEYR 2640 T(715-721) S T (704-710) (716-722) (716-722) (714-720) SASTGAS 2641SETAGST 2651 NGTSGG 2661 NSTSGG 2671 NGTSGGS 2681 (262-268) (263-269) ATSS T (263-270) (262-269) (262-269) VFMIPQY 2642 VFMIPQY 2652 VFMIPQY2662 VFMIPQY 2672 VFMVPQY 2682 GYL GYL GYL GYL GYL (370-379) (371-380)(372-381) (371-380) (371-380) NQSGSA 2643 NPGGTA 2653 TTGGTA 2663 INGSGQ2673 QTTGTGG 2683 QNK GNR NTQ NQQ TQ (451-459) (453-461) (453-461)(451-459) (451-459) SV 2644 AN 2654 AN 2664 AV 2674 AN 2684 (472-473)(474-475) (474-475) (472-473) (472-473) KTDNNN 2645 LDQNNNS 2655 TGQNNN2665 VTQNNN 2675 TNQNNNS 2685 SN N SN SE N (493-500) (495-502) (495-502)(493-500) (493-500) KDDKDK 2646 KDDEDRF 2656 KDDEER 2666 KEGEDR 2676KDDDDRF 2686 F (530-536) F F (528-534) (528-534) (530-536) 5(528-34)SAGASN 2647 GATNKT 2657 NAARDN 2667 GTGRDN 2677 GAGNDG 2687 (547-552)(549-554) (549-554) (547-552) (547-552) STDPATG 2648 NTAAQTQ 2658NTAPQIG 2668 QAQAQT 2678 NTQAQTG 2688 DVH VVN TVNS GWVQ LVH (588-897)(589-598) (590-600) (588-597) (588-597) AN 2649 TG 2659 TS 2669 NN 2679TN 2689 (709-710) (710-711) (711-712) (709-710) (709-710) DNNGLY 2650DSQGVY 2660 NTEGVY 2670 NTEGVY 2680 NTEGVYS 2690 T S S S (716-722)(716-722) (717-723) (718-724) (716-722) NGTSGGS 2691 NGTSGG 2701 RLGTTSS2711 RIGTTAN 2721 RLGTTSNS 2731 T ST S S (253-260) (263-270) (263-270)(253-260) (262-269) VFMIPQY 2692 VFMIPQY 2702 VFMVPQ 2712 VFMVPQ 2722VFMVPQYG 2732 GYL GYL YGYC YGYC YC (372-381) (372-381) (360-369)(369-378) (360-369) STGGTAG 2693 STGGTQ 2703 GETLNQ 2713 GNSLNQ 2723GETLNQGN 2733 TQ GTQ GNA GTA A (453-461) (453-461) (444-452) (453-461)(444-452) SA 2694 SA 2704 AF 2714 AY 2724 AF 2734 (474-475) (474-475)(465-466) (474-475) (465-466) LSQNNNS 2695 LSQNNNS 2705 ASQNYKI 2715ANQNYKI 2725 ASQNYKIPA 2735 N N PASGG PASGG SGG (495-502) (495-502)(486-497) (495-506) (486-497) KDDEERF 2696 KDDEERF 2706 GPSDGD 2716GAGDSD 2726 GPSDGDF 2736 (530-536) (530-536) F F (526-532) (526-532)(535-541) GAGKDN 2697 GAGRDN 2707 VTGNTT 2717 PSGNTT 2727 VTGNTT 2737(549-554) (549-554) (544-549) (553-558) (544-549) NAAPIVG 2698 NTGPIVG2708 TTAPITG 2718 TTAPHIA 2728 TTAPITGNV 2738 AVN NVN NVT NLD T(590-599) (590-599) (585-594) (594-503) (585-594) TN 2699 TN 2709 SS2719 NS 2729 SS 2739 (711-712) (711-712) (706-707) (715-716) (706-707)NTDGTYS 2700 NTEGTYS 2710 DTTGKYT 2720 DNAGNY 2730 DTTGKYT 2740(718-724) (718-724) (713-719) H (713-719) SEQ SEQ Bovine AAV (amino acidID ID numbers) NO Avian AAV (amino acid numbers) NO RLGSSNAS 2741RIQGPSGG 2751 (255-262) (265-272) VFMVPQYGYC 2742 ITIPQYGYC 2752(362-371) (375-384) GGTLNQGNS 2743 VSQAGSSGR 2753 (447-455) (454-462) SG2744 AA 2754 (468-469) (475-476) ASQNYKIPQGRN 2745 ASNITKNNVFSV 2755(489-500) (496-507) ANDATDF 2746 FSGEPDR 2756 (529-535) (533-539) ITGNTT2747 VYDQTTAT 2757 (547-552) (552-559) TTVPTVDDVD 2748 VTPGTRAAVN 2758(588-597) (595-604) DS 2749 AD 2759 (709-710) (716-717) DNAGAYK 2750SDTGSYS 2760 (716-722) (723-729)

In some embodiments, the amino acid substitution replaces any eightamino acids in an AAV capsid protein subunit from any one of thefollowing serotypes: AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8,AAV9, AAVrh8, AAVrh10, AAV10, AAV11, AAV12, AAVrh32.22, bovine AAV, orAvian AAV. For example, the amino acid substitution may replace thefollowing amino acids (VP1 numbering): 355-362, 363-370, 371-378,379-386, 387-394, 395-402, 403-410, 411-418, 419-426, 427-434, 435-442,443-450, 451-458, 459-466, 467-474, 475-482, 483-490, 491-498, 499-506,507-514, 515-522, 523-530, 531-538, 539-546, 547-554, 555-562, 563-570,571-578, 579-586, 587-594, 595-602, 603-610, 611-618, 619-626, 627-634,635-642, 643-650, 651-658, 659-666, 667-674, 675-682, 683-690, 691-698,699-706, 707-714, 715-722 in any of the above-listed AAV serotypes.

In some embodiments, the amino acid substitution is selected from anyone of SEQ ID NO: 19-20. In some embodiments, the amino acidsubstitution has at least 95%, at least 96%, at least 97%, at least 98%,or at least 99% sequence identity with any one of SEQ ID NO: 12-18. Insome embodiments, the substitution is at the amino acids correspondingto amino acids 587-594 of the wildtype AAV9 capsid protein subunit. Insome embodiments, the substitution is at the amino acids correspondingto amino acids 587-594 of the wildtype AAV1 capsid protein subunit. Insome embodiments, the substitution is at the amino acids correspondingto amino acids 587-594 of the wildtype AAV6 capsid protein subunit. Insome embodiments, the substitution is at the amino acids correspondingto amino acids 589-596 of the wildtype AAV8 capsid protein subunit. Insome embodiments, the substitution is at the amino acids correspondingto amino acids 587-594 of the wildtype AAVrh8 capsid protein subunit. Insome embodiments, the substitution is at the amino acids correspondingto amino acids 589-596 of the wildtype AAVrh10 capsid protein subunit.

In some embodiments, the amino acid substitution is selected from anyone of SEQ ID NO: 18-20. In some embodiments, the amino acidsubstitution has at least 95%, at least 96%, at least 97%, at least 98%,or at least 99% sequence identity with any one of SEQ ID NO: 18-20. Insome embodiments, the substitution is at the amino acids correspondingto amino acids 451-458 of the wildtype AAV9 capsid protein subunit.

In some embodiments, an amino acid deletion comprises a deletion of atleast one, at least two, at least three, at least four, at least five,at least six, at least seven, at least eight, at least nine, or at leastten amino acids compared to the wildtype capsid protein subunit.

In some embodiments, an AAV capsid protein subunit comprises one or moreamino acid substitutions and one or more amino acid deletions. In someembodiments, a capsid protein subunit comprises at least one amino acidsubstitution and at least one amino acid deletion. In some embodiments,a capsid protein subunit comprises at least one amino acid substitutionand at least one amino acid deletion, wherein the at least one aminoacid substitution and the at least one amino acid deletion areimmediately adjacent to one another in the capsid protein subunit aminoacid sequence.

In some embodiments, the capsid protein subunits are modified to producean AAV capsid protein subunit that, when present in an AAV virusparticle or AAV virus vector, has a phenotype of selectively targetingthe CNS (e.g., the brain, the spinal cord). In some embodiments, thecapsid protein subunits are modified to produce an AAV capsid proteinsubunit that, when present in an AAV virus particle or AAV virus vector,has a phenotype of evading neutralizing antibodies. The AAV virus-likeparticle or AAV vector can also have a phenotype of enhanced ormaintained transduction efficiency in addition to the phenotype ofevading neutralizing antibodies and/or targeting the CNS.

In some embodiments, the one or more substitutions can introduce one ormore sequences from a capsid protein subunit of a first AAV serotypeinto the capsid protein subunit of a second AAV serotype that isdifferent from the first AAV serotype.

The base AAV capsid protein subunit to which modifications are added canbe a capsid protein subunit of an AAV serotype selected from AAV1, AAV2,AAV3, AAV3B, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12,AAVrh.8, AAVrh.10, AAVrh.32.33, AAVrh74, bovine AAV, avian AAV or anyother AAV now known or later identified. In some embodiments, the baseAAV capsid protein subunit is of the AAV9 serotype. In some embodiments,the base AAV capsid protein subunit is chimeric. In some embodiments,the base AAV capsid protein subunit is an AAV8/9 chimera.

Several examples of a modified AAV capsid protein subunit are providedherein. In the following examples, the capsid protein subunit cancomprise the specific substitutions described and, in some embodiments,can comprise fewer or more substitutions than those described. As usedherein, “substitution” may refer to a single amino acid substitution, ora substitution of more than one contiguous amino acid. For example insome embodiments, a capsid protein subunit can comprise at least 1, 2,3, 4, 5, 6, 7, 8, 9, 10, etc., single amino acid substitutions. In someembodiments, a capsid protein subunit can comprise one or moresubstitutions of multiple contiguous amino acids, such as one or moresubstitutions of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 contiguous aminoacids.

Furthermore, in some embodiments described herein wherein an amino acidresidue is substituted by any amino acid residue other than the aminoacid residue present in the wildtype or native amino acid sequence, theany other amino acid residue can be any natural or non-natural aminoacid residue known in the art (see, e.g., Tables 2 and 4). In someembodiments, the substitution can be a conservative substitution and insome embodiments, the substitution can be a nonconservativesubstitution. In some embodiments, an AAV capsid protein subunitcomprises one or more amino acid substitutions, wherein the amino acidsubstitutions are each individually selected from SEQ ID NO: 12-18 asshown in Table 7.1.

TABLE 7.1 AMINO ACID SUBSTITUTIONS Amino Acid  SEQ ID Substitution NO.SCQPTVMN 12 FGVPNQPL 13 QRGQAAPF 14 GDYAPIRE 15 KTRRIVQH 16 FGFPNQPL 17RQDQPINA 18

In some embodiments, an AAV capsid protein subunit comprises one or moreamino acid substitutions, wherein the amino acid substitutions are eachselected from SEQ ID NO: 19-20 as shown in Table 7.2.

TABLE 7.2 AMINO ACID SUBSTITUTIONS Amino Acid  SEQ ID Substitution NO.SKVESWTE 19 STVDSIAI 20

In some embodiments, an AAV capsid protein subunit may comprise a firstsubstitution selected from the sequences listed in Table 7.1 and asecond substitution selected from the sequences listed in Table 7.2. Insome embodiments, an AAV capsid protein subunit may comprise a firstsubstitution, a second substitution as shown in Tables 7.3 and 7.4.

TABLE 7.3 COMBINATIONS OF AMINO ACID SUBSTITUTIONS First SubstitutionSecond Substitution (SEQ ID NO) (SEQ ID NO) 12, 13, 14, 15, 16, 17, 19or 20 or 18

TABLE 7.4 COMBINATIONS OF AMINO ACID SUBSTITUTIONS First SubstitutionSecond Substitution (SEQ ID NO) (SEQ ID NO) 12 19 12 20 13 19 13 20 1419 14 20 15 19 15 20 16 19 16 20 17 19 17 20 18 19 18 20

In some embodiments, an AAV capsid protein subunit comprises an aminoacid modification (e.g., substitution and/or deletion), wherein theamino acid modification modifies one or more surface-exposed regions,such as an antigenic region, on the AAV capsid protein subunit.

In some embodiments, an AAV capsid protein subunit comprises one or moreamino acid substitutions, wherein at least one of the amino acidsubstitutions comprises one of SEQ ID NOs: 19-20. In some embodiments,the substitution replaces the amino acids corresponding to amino acids587-594 of the wildtype AAV9 capsid protein subunit.

In some embodiments, an AAV capsid protein subunit comprises one or moreamino acid substitutions, wherein at least one of the amino acidsubstitutions comprises one of SEQ ID NOs: 12-18. In some embodiments,the substitution replaces the amino acids corresponding to amino acids451-458 of the wildtype AAV9 capsid protein subunit.

In some embodiments, an AAV capsid protein subunit comprises asubstitution comprising a sequence of eight amino acids(X¹-X²-X³-X⁴-X⁵-X⁶-X⁷-X⁸) (SEQ ID NO: 158) that does not occur in thenative capsid protein subunit sequence. In some embodiments, X¹ is notI, X² is not N, X³ is not G, X⁴ is not S, X⁵ is not G, X⁶ is not Q, X⁷is not N, and/or X⁸ is not Q. In some embodiments, X¹ is S, F, Q, G, K,or R. In some embodiments, X² is C, G, R, D, T, or Q. In someembodiments, X³ is Q, V, G, Y, R, F, or D. In some embodiments, X⁴ is P,Q, A, or R. In some embodiments, X⁵ is T, N, A, P, or I. In someembodiments, X⁶ is V, Q, A, or I. In some embodiments, X⁷ is M, P, R, Q,or N. In some embodiments, X⁸ is N, L, F, E, H, or A. In someembodiments, X¹ is S, X² is C, X³ is Q, X⁴ is P, X⁵ is T, X⁶ is V, X⁷ isM, and X⁸ is N. In some embodiments, X¹ is F, X² is G, X³ is V, X⁴ is P,X⁵ is N, X⁶ is Q, X⁷ is P, and X⁸ is L. In some embodiments, X¹ is Q, X²is R, X³ is G, X⁴ is Q, X⁵ is A, X⁶ is A, X⁷ is P, and X⁸ is F. In someembodiments, X¹ is G, X² is D, X³ is Y, X⁴ is A, X⁵ is P, X⁶ is I, X⁷ isR, and X⁸ is E. In some embodiments, X¹ is K, X² is T, X³ is R, X⁴ is R,X⁵ is I, X⁶ is V, X⁷ is Q, and X⁸ is H. In some embodiments, X¹ is F, X²is G, X³ is F, X⁴ is P, X⁵ is N, X⁶ is Q, X⁷ is P, and X⁸ is L. In someembodiments, X¹ is R, X² is Q, X³ is D, X⁴ is Q, X⁵ is P, X⁶ is I, X⁷ isN, and X⁸ is A.

In some embodiments, X¹ is not A, X² is not Q, X³ is not A, X⁴ is not Q,X⁵ is not A, X⁶ is not Q, X⁷ is not T, and/or X⁸ is not G. In someembodiments, X¹ is S. In some embodiments, X² is K or T. In someembodiments, X³ is V. In some embodiments, X⁴ is E or D. In someembodiments, X⁵ is S. In some embodiments, X⁶ is W or I. In someembodiments, X⁷ is T or A. In some embodiments, X⁸ is E or I. In someembodiments, X¹ is S, X² is K, X³ is V, X⁴ is E, X⁵ is S, X⁶ is W, X⁷ isT, and X⁸ is E. In some embodiments, X¹ is S, X² is T, X³ is V, X⁴ is D,X⁵ is S, X⁶ is I, X⁷ is A, and X⁸ is I.

In some embodiments, an AAV subunit protein comprises one or more aminoacid deletions, wherein the amino acid deletion comprises a deletion ofat least six or at least eight amino acids compared to the wildtype AAVcapsid protein subunit. In some embodiments, an AAV capsid proteinsubunit comprises a deletion of eight consecutive amino acids comparedto the native capsid protein subunit sequence. In some embodiments, anAAV capsid protein subunit comprises a deletion of six consecutive aminoacids compared to the native capsid protein subunit sequence.

In some embodiments, an AAV capsid protein subunit comprises thesequence LSKTQTLK (SEQ ID NO: 1374) or the sequence LSKTDPQTLK (SEQ IDNO: 1375). In some embodiments, the AAV capsid protein subunitcomprising SEQ ID NO: 1374 or 1375 is of a serotype selected from AAV1,AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12,AAVrh8, AAVrh10, AAVrh32.33, AAVrh74, Avian AAV and Bovine AAV.

In some embodiments, an AAV capsid protein subunit comprises a firstsubstitution comprising a sequence selected from SEQ ID NO: 12-18; and asecond substitution comprising a sequence selected from SEQ ID NO:19-20.

In some embodiments, an AAV capsid protein subunit comprises an aminoacid deletion and a substitution, wherein the substitution comprises asequence selected from SEQ ID NO: 12-20.

In some embodiments, a recombinant capsid protein subunit has a sequencethat is at least 90%, at least 95%, at least 96%, at least 97%, at least98%, at least 99% or 100% identical to SEQ ID NO: 9 (AAV9) and comprisesone or more of the following amino acid substitutions: I451S, I451F,I451Q, I451G, I451K, 1451R, N452C, N452G, N452R, N452D, N452T, N452Q,G453Q, G453V, G453Y, G453R, G453F, G453D, S454P, S454Q, S454A, S454R,G455T, G455N, G455A, G455P, G4551, Q456V, Q456A, Q4561, N457M, N457P,N457R, N457Q, Q458N, Q458L, Q458F, Q458E, Q458H, Q458A, A587S, Q588K,Q588T, A589V, Q590E, Q590D, A591 S, Q592W, Q5921, T593A, G594E, G594I.

Any of the AAV capsid protein subunits described herein may furthercomprise a modification (e.g., a substitution or a deletion) in the HIloop. The HI loop is a prominent domain on the AAV capsid proteinsubunit surface, between β strands βH and βI that extends from eachviral protein (VP) subunit overlapping the neighboring fivefold VP. Insome embodiments, an AAV capsid protein subunit comprises one, two,three, four, five, six, seven, or eight amino acid substitutions in theHI loop. In some embodiments, the AAV capsid protein subunit comprisesone or more of the following substitutions in the HI loop: P661R, T662S,Q666G, S667D, wherein the numbering corresponds to the wildtype AAV8capsid protein subunit (SEQ ID NO: 8). In some embodiments, the AAVcapsid protein subunit comprises one or more of the followingsubstitutions in the HI loop: P659R, T660S, A661T, K664G, wherein thenumbering corresponds to the wildtype AAV9 capsid protein subunit (SEQID NO: 9).

In some embodiments, an AAV capsid protein subunit comprises one, two,three, or four amino acid substitutions, wherein each substitutionmodifies a different antigenic site on the AAV capsid protein subunit,and wherein at least one of the amino acid substitutions modifies the HIloop of the capsid protein subunit.

In some embodiments, an AAV capsid protein subunit comprises a first, asecond, a third, and a fourth amino acid substitution. In someembodiments, at least one of the substitutions modifies the HI Loop ofthe capsid protein subunit. In some embodiments, the AAV capsid proteinsubunit comprises one or more of the following substitutions in the HIloop: P661R, T662S, Q666G, S667D, wherein the numbering corresponds tothe wildtype AAV8 capsid protein subunit (SEQ ID NO: 8); or P659R,T660S, A661T, K664G, wherein the numbering corresponds to the wildtypeAAV9 capsid protein subunit (SEQ ID NO: 9). In some embodiments, an AAVcapsid protein subunit comprises the amino acid sequence of any one ofSEQ ID NO: 185-187. In some embodiments, an AAV capsid protein subunitcomprises an amino acid sequence sharing at least 90%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% sequence identityto any one of SEQ ID NO: 165-187.

Also provided herein is a nucleic acid, or a plasmid comprising the samethat encodes one or more of the AAV capsid protein subunits describedherein. The nucleotide sequence may be a DNA sequence or an RNAsequence. In some embodiments, cell comprises one or more nucleic acidsor plasmids described herein.

In some embodiments, an AAV protein capsid comprises an AAV capsidprotein subunit as described herein. Further provided herein is a viralvector comprising an AAV protein capsid as well as a compositioncomprising the AAV protein capsid, AAV capsid protein subunit and/orviral vector in a pharmaceutically acceptable carrier.

In some embodiments, modification of one or more antigenic sites resultsin reduced binding by an antibody to the one or more antigenic sites. Insome embodiments, modification of the one or more antigenic sitesresults in inhibition of neutralization of infectivity of a virusparticle comprising the AAV capsid protein subunit.

As described herein, the nucleic acid and amino acid sequences of thecapsid protein subunits from a number of AAV are known in the art. Thus,the amino acids “corresponding” to amino acid positions of the nativeAAV capsid protein subunits can be readily determined for any other AAV(e.g., by using sequence alignments).

The modified capsid protein subunits can be produced by modifying thecapsid protein subunit of any AAV now known or later discovered.Further, the base AAV capsid protein subunit that is to be modified canbe a naturally occurring AAV capsid protein subunit (e.g., an AAV2,AAV3a or 3b, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10 or AAV11 capsidprotein subunit or any of the AAV shown in Table 2) but is not solimited. Those skilled in the art will understand that a variety ofmanipulations to the AAV capsid protein subunits are known in the artand the disclosure is not limited to modifications of naturallyoccurring AAV capsid protein subunits. For example, the capsid proteinto be modified may already have alterations as compared with naturallyoccurring AAV (e.g., is derived from a naturally occurring AAV capsidprotein subunit, e.g., AAV2, AAV3a, AAV3b, AAV4, AAV5, AAV6, AAV7, AAV8,AAV9, AAV10, AAV11, AAV12 or any other AAV now known or laterdiscovered). In some embodiments, the capsid protein subunit may be achimeric capsid protein subunit. In some embodiments, the capsid proteinsubunit may be an engineered AAV, such as AAV2i8, AAV2g9, AAV-LK03,AAV7m8, AAV Anc80, AAV PHP.B.

Thus, in some embodiments, the AAV capsid protein subunit to be modifiedcan be derived from a naturally occurring AAV but further comprises oneor more foreign sequences (e.g., that are exogenous to the native virus)that are inserted and/or substituted into the capsid protein subunitand/or has been altered by deletion of one or more amino acids.

Accordingly, when referring herein to a specific AAV capsid proteinsubunit (e.g., an AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10or AAV11 capsid protein subunit or a capsid protein subunit from any ofthe AAV shown in Table 2, etc.), it is intended to encompass the nativecapsid protein subunit as well as capsid protein subunits that havealterations other than the modifications described herein. Suchalterations include substitutions, insertions and/or deletions. In someembodiments, the capsid protein subunit comprises 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20, less than 20, lessthan 30, less than 40, less than 50, less than 60, or less than 70 aminoacids inserted therein (other than the insertions described herein) ascompared with the native AAV capsid protein subunit sequence. In someembodiments, the capsid protein subunit comprises 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20, less than 20, lessthan 30, less than 40, less than 50, less than 60, or less than 70 aminoacid substitutions (other than the amino acid substitutions describedherein) as compared with the native AAV capsid protein subunit sequence,in some embodiments, the capsid protein subunit comprises a deletion of1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20,less than 20, less than 30, less than 40, less than 50, less than 60, orless than 70 amino acids as compared with the native AAV capsid proteinsubunit sequence.

In some embodiments, the AAV capsid protein subunit has an amino acidsequence that is at least about 90%, about 95%, about 97%, about 98% orabout 99% similar or identical to a native AAV capsid protein subunitsequence.

Methods of determining sequence similarity or identity between two ormore amino acid sequences are known in the art. Sequence similarity oridentity may be determined for an entire length of a nucleic acid or foran indicated portion of a nucleic acid. Sequence similarity or identitymay be determined using standard techniques, including, but not limitedto, the local sequence identity algorithm of Smith & Waterman, Adv.Appl. Math. 2, 482 (1981), by the sequence identity alignment algorithmof Needleman & Wunsch, J Mol. Biol. 48,443 (1970), by the search forsimilarity method of Pearson & Lipman, Proc. Natl. Acad. Sci. USA 85,2444 (1988), by computerized implementations of these algorithms (GAP,BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package,Genetics Computer Group, 575 Science Drive, Madison, WI), the Best Fitsequence program described by Devereux et al., Nucl. Acid Res. 12,387-395 (1984), or by inspection.

Another suitable algorithm is the BLAST algorithm, described in Altschulet al., J Mol. Biol. 215, 403-410, (1990) and Karlin et al., Proc. Natl.Acad. Sci. USA 90, 5873-5787 (1993). A particularly useful BLAST programis the WU-BLAST-2 program which was obtained from Altschul et al.,Methods in Enzymology, 266, 460-480 (1996);http://blast.wustl/edu/blast/README.html. WU-BLAST-2 uses several searchparameters, which are optionally set to the default values. Theparameters are dynamic values and are established by the program itselfdepending upon the composition of the particular sequence andcomposition of the particular database against which the sequence ofinterest is being searched; however, the values may be adjusted toincrease sensitivity.

Further, an additional useful algorithm is gapped BLAST as reported byAltschul et al, (1997) Nucleic Acids Res. 25, 3389-3402.

For purposes of the instant disclosure, unless otherwise indicated,percent identity is calculated using the Basic Local Alignment SearchTool (BLAST) available online at blast.ncbi.nlm.nih.gov/Blast.cgi. Theskilled artisan will understand that other algorithms may be substitutedas appropriate.

In some embodiments, a protein capsid comprises a modified AAV capsidprotein subunit as described herein. In some embodiments, the proteincapsid is a parvovirus capsid, which may further be an autonomousparvovirus capsid or a dependovirus capsid. Optionally, the proteincapsid is an AAV protein capsid. In some embodiments, the AAV proteincapsid is an AAV1, AAV2, AAV3a, AAV3b, AAV4, AAV5, AAV6, AAV7, AAV8,AAV9, AAV10, AAV11, AAV12, AAVrh8, AAVrh10, AAVrh32.33, bovine AAVprotein capsid, avian AAV protein capsid or any other AAV now known orlater identified. A nonlimiting list of AAV serotypes is shown in Table2. An AAV protein capsid can be any AAV serotype listed in Table 2 orderived from any of the foregoing by one or more insertions,substitutions and/or deletions. Molecules that can be packaged by themodified virus protein capsid and transferred into a cell includetransfer cassettes (e.g., heterologous DNA or RNA), polypeptides, smallorganic molecules, metals, or combinations of the same.

Heterologous molecules are defined as those that are not naturally foundin an AAV infection, e.g., those not encoded by a wild-type AAV genome.Further, therapeutically useful molecules can be associated with theoutside of the chimeric protein capsid for transfer of the moleculesinto host target cells. Such associated molecules can include DNA, RNA,small organic molecules, metals, carbohydrates, lipids and/orpolypeptides. In some embodiments the therapeutically useful molecule iscovalently linked (i.e., conjugated or chemically coupled) to theprotein capsid or a capsid protein thereof. Methods of covalentlylinking molecules are known by those skilled in the art.

The modified protein capsids also find use in raising antibodies againstthe novel protein capsid structures. As a further alternative, anexogenous amino acid sequence may be inserted into the modified proteincapsid or capsid protein subunit thereof for antigen presentation to acell, e.g., for administration to a subject to produce an immuneresponse to the exogenous amino acid sequence.

In some embodiments, the protein capsids can be administered to blockcertain cellular sites prior to and/or concurrently with (e.g., withinminutes or hours of each other) administration of a virus vectordelivering a nucleic acid encoding a polypeptide or functional RNA ofinterest. For example, the inventive protein capsids can be delivered toblock cellular receptors on liver cells and a delivery vector (e.g., anAAV vector) can be administered subsequently or concurrently, which mayreduce transduction of liver cells, and enhance transduction of othertargets (e.g., skeletal, cardiac and/or diaphragm muscle).

According to some embodiments, modified protein capsids can beadministered to a subject prior to and/or concurrently with a modifiedvirus vector as described herein. Further, the disclosure providescompositions and pharmaceutical formulations comprising the inventivemodified protein capsids or capsid protein subunit thereof; optionally,the composition also comprises a modified virus vector as describedherein.

In some embodiments, a nucleic acid (optionally, an isolated nucleicacid) encodes the modified protein capsid subunits described herein.Further provided are nucleic acids, and cells (in vivo or in culture)comprising the nucleic acids and/or virus vectors described herein. Asone example, a virus vector may comprise: (a) a protein capsidcomprising a modified AAV capsid protein subunit as described herein;and (b) a nucleic acid comprising at least one terminal repeat sequence,wherein the nucleic acid is encapsidated by the AAV protein capsid.

Suitable viral vectors include, for example, adenovirus, AAV,herpesvirus, vaccinia, poxviruses, baculovirus, lentivirus, coronavirus,and the like. Suitable nucleic acids include, but are not limited to,plasmids, phage, YACs, BACs, and the like. Such nucleic acids and cellscan be used, for example, as reagents (e.g., helper packaging constructsor packaging cells) for the production of modified virus proteincapsids, protein capsid subunits, or virus vectors as described herein.

Protein capsids and capsid protein subunits described herein can beproduced using any method known in the art, e.g., by using a baculovirussystem (Brown et al., (1994) Virology 198:477-488).

The modifications to the AAV capsid protein subunit as described hereinare “selective” modifications. This approach is in contrast to previouswork with whole subunit or large domain swaps between AAV serotypes(see, e.g., international patent publication WO 00/28004 and Hauck etal., (2003) J. Virology 77:2768-2774). In some embodiments, a“selective” modification results in the insertion and/or substitutionand/or deletion of less than or equal to about 20, 18, 15, 12, 10, 9, 8,7, 6, 5, 4 or 3 contiguous amino acids.

The modified capsid protein subunits and protein capsids describedherein can further comprise any other modification, now known or lateridentified. For example, the AAV capsid protein subunits and proteincapsids can be chimeric in that they can comprise all or a portion of acapsid protein subunit from another virus, optionally another parvovirusor AAV, e.g., as described in international patent publication WO00/28004.

In some embodiments, the protein capsid or capsid protein subunit can bea targeted protein capsid or capsid protein subunit, comprising atargeting sequence (e.g., substituted or inserted in the protein capsidor capsid protein subunit) that directs the protein capsid or capsidprotein subunit to interact with cell-surface molecules present ondesired target tissue(s) (see, e.g., International patent publication WO00/28004 and Hauck et al., (2003) J. Virology 77:2768-2774); Shi et al.,Human Gene Therapy 17:353-361 (2006) [describing insertion of theintegrin receptor binding motif RGD at positions 520 and/or 584 of theAAV capsid protein subunit]; and U.S. Pat. No. 7,314,912 [describinginsertion of the PI peptide containing an RGD motif following amino acidpositions 447, 534, 573 and 587 of the AAV2 capsid protein subunit]).Other positions within the AAV capsid protein subunit that tolerateinsertions are known in the art (e.g., positions 449 and 588 describedby Grifman et al., Molecular Therapy 3:964-975 (2001)).

For example, a protein capsid or capsid protein subunit as describedherein may have relatively inefficient tropism toward certain targettissues of interest (e.g., liver, skeletal muscle, heart, diaphragmmuscle, kidney, brain, stomach, intestines, skin, endothelial cells,and/or lungs). A targeting sequence can advantageously be incorporatedinto these low-transduction vectors to thereby confer to the proteincapsid (or a capsid protein subunit thereof) a desired tropism and,optionally, selective tropism for particular tissue(s). AAV capsidprotein subunits, protein capsids and AAV vectors comprising targetingsequences are described, for example in international patent publicationWO 00/28004. As another example, one or more non-naturally occurringamino acids as described by Wang et al., Annu Rev Biophys Biomol Struct.35:225-49 (2006)) can be incorporated into an AAV capsid protein subunitas described herein at an orthogonal site as a means of redirecting alow-transduction vector to desired target tissue(s). These unnaturalamino acids can advantageously be used to chemically link molecules ofinterest to the AAV capsid protein subunit including without limitation:glycans (mannose-dendritic cell targeting); RGD, bombesin or aneuropeptide for targeted delivery to specific cancer cell types; RNAaptamers or peptides selected from phage display targeted to specificcell surface receptors such as growth factor receptors, integrins, andthe like.

In some embodiments, the targeting sequence may be a capsid proteinsubunit sequence (e.g., an autonomous parvovirus capsid sequence, AAVcapsid protein subunit sequence, or any other viral capsid sequence)that directs infection to a particular cell type(s).

As another nonlimiting example, a heparin or heparan sulfate bindingdomain (e.g., the respiratory syncytial virus heparin binding domain)may be inserted or substituted into a capsid protein subunit that doesnot typically bind HS receptors (e.g., AAV4, AAV5) to confer heparinand/or heparan sulfate binding to the resulting mutant.

B19 infects primary erythroid progenitor cells using globoside as itsreceptor (Brown et al, (1993) Science 262: 114). The structure of B19has been determined to 8 Å resolution (Agbandje-McKenna et al, (1994)Virology 203: 106). The region of the B19 capsid that binds to globosidehas been mapped between amino acids 399-406 (Chapman et al, (1993)Virology 194:419), a looped out region between β-barrel structures E andF (Chipman et al, (1996) Proc. Nat. Acad. Sci. USA 93:7502).Accordingly, the globoside receptor binding domain of the B19 capsid maybe substituted into an AAV capsid protein subunit to target a proteincapsid or virus vector comprising the same to erythroid cells.

In some embodiments, the exogenous targeting sequence may be any aminoacid sequence encoding a peptide that alters the tropism of a proteincapsid or virus vector comprising the modified AAV capsid proteinsubunit. In some embodiments, the targeting peptide or protein may benaturally occurring or, alternately, completely or partially synthetic.Exemplary targeting sequences include ligands and other peptides thatbind to cell surface receptors and glycoproteins, such as ROD peptidesequences, bradykinin, hormones, peptide growth factors (e.g., epidermalgrowth factor, nerve growth factor, fibroblast growth factor,platelet-derived growth factor, insulin-like growth factors I and II,etc.), cytokines, melanocyte stimulating hormone (e.g., a, β or γ),neuropeptides and endorphins, and the like, and fragments thereof thatretain the ability to target cells to their cognate receptors. Otherillustrative peptides and proteins include substance P, keratinocytegrowth factor, neuropeptide Y, gastrin releasing peptide, interleukin 2,hen egg white lysozyme, erythropoietin, gonadolibcrin, corticostatin,β-endorphin, leu-enkephalin, rimorphin, alpha-neo-enkephalin,angiotensin, pneumadin, vasoactive intestinal peptide, neurotensin,motilin, and fragments thereof as described above. As yet a furtheralternative, the binding domain from a toxin (e.g., tetanus toxin orsnake toxins, such as alpha-bungarotoxin, and the like) can besubstituted into the capsid protein subunit as a targeting sequence. Insome embodiments, the AAV capsid protein subunit can be modified bysubstitution of a “nonclassical” import/export signal peptide (e.g.,fibroblast growth factor-1 and -2, interleukin 1, HIV-1 Tat protein,herpes virus VP22 protein, and the like) as described by Cleves (CurrentBiology 7:R318 (1997)) into the AAV capsid protein subunit. Alsoencompassed are peptide motifs that direct uptake by specific cells,e.g., a FVFLP (SEQ ID NO: 22) peptide motif triggers uptake by livercells.

Phage display techniques, as well as other techniques known in the art,may be used to identify peptides that recognize any cell type ofinterest.

The targeting sequence may encode any peptide that targets to a cellsurface binding site, including receptors (e.g., protein, carbohydrate,glycoprotein or proteoglycan). Examples of cell surface binding sitesinclude, but are not limited to, heparan sulfate, chondroitin sulfate,and other glycosaminoglycans, sialic acid moieties found on mucins,glycoproteins, and gangliosides, MHC 1 glycoproteins, carbohydratecomponents found on membrane glycoproteins, including, mannose,N-acetyl-galactosamine, N-acetyl-glucosamine, fucose, galactose, and thelike.

In some embodiments, a heparan sulfate (HS) or heparin binding domain issubstituted into the capsid protein subunit (for example, in an AAVprotein capsid subunit that otherwise does not bind to HS or heparin).It is known in the art that HS/heparin binding is mediated by a “basicpatch” that is rich in arginines and/or lysines. In some embodiments, asequence following the motif BXXB (SEQ ID NO: 23), where “B” is a basicresidue and X is neutral and/or hydrophobic residue can be employed. Asa nonlimiting example, BXXB can be RGNR (SEQ ID NO: 24). As anothernonlimiting example, BXXB is substituted for amino acid positions 262through 265 in the native AAV2 capsid protein subunit or at thecorresponding position(s) in the capsid protein subunit of another AAVserotype.

Table 8 shows other non-limiting examples of suitable targetingsequences.

TABLE 8 TARGETING SEQUENCES SEQ ID Sequence NO Reference NSVRDL(G/S)  25Muller et al., Nature Biotechnology 21: 1040-1046 (2003) PRSVTVP  26Muller et al., Nature Biotechnology 21: 1040-1046 (2003) NSVSSX(S/A)  27Muller et al., Nature Biotechnology 21: 1040-1046 (2003) NGR, NGRAHA  28Grifman et al., Molecular Therapy 3: 964-975 (2001) QPEHSST  29Work et al., Molecular Therapy 13: 683-693 (2006) VNTANST  30Work et al., Molecular Therapy 13: 683-693 (2006) HGPMQS  31Work et al., Molecular Therapy 13: 683-693 (2006) PHKPPLA  32Work et al., Molecular Therapy 13: 683-693 (2006) IKNNEMW  33Work et al., Molecular Therapy 13: 683-693 (2006) RNLDTPM  34Work et al., Molecular Therapy 13: 683-693 (2006) VDSHRQS  35Work et al., Molecular Therapy 13: 683-693 (2006) YDSKTKT  36Work et al., Molecular Therapy 13: 683-693 (2006) SQLPHQK  37Work et al., Molecular Therapy 13: 683-693 (2006) STMQQNT  38Work et al., Molecular Therapy 13: 683-693 (2006) TERYMTQ  39Work et al., Molecular Therapy 13: 683-693 (2006) QPEHSST  40Work et al., Molecular Therapy 13: 683-693 (2006) DASLSTS  41Work et al., Molecular Therapy 13: 683-693 (2006) DLPNKT  42Work et al., Molecular Therapy 13: 683-693 (2006) DLTAARL  43Work et al., Molecular Therapy 13: 683-693 (2006) EPHQFNY  44Work et al., Molecular Therapy 13: 683-693 (2006) EPQSNHT  45Work et al., Molecular Therapy 13: 683-693 (2006) MSSWPSQ  46Work et al., Molecular Therapy 13: 683-693 (2006) NPKHNAT  47Work et al., Molecular Therapy 13: 683-693 (2006) PDGMRTT  48Work et al., Molecular Therapy 13: 683-693 (2006) PNNNKTT  49Work et al., Molecular Therapy 13: 683-693 (2006) QSTTHDS  50Work et al., Molecular Therapy 13: 683-693 (2006) TGSKQKQ  51Work et al., Molecular Therapy 13: 683-693 (2006) SLKHQAL  52Work et al., Molecular Therapy 13: 683-693 (2006) SPIDGEQ  53Work et al., Molecular Therapy 13: 683-693 (2006) WIFPWIQL  54Hajitou et al., TCM 16: 80-88 (2006) CDCRGDCFC  55Hajitou et al., TCM 16: 80-88 (2006) CNGRC  56Hajitou et al., TCM 16: 80-88 (2006) CPRECES  57Hajitou et al., TCM 16: 80-88 (2006) CTTHWGFTLC  58Hajitou et al., TCM 16: 80-88 (2006) CGRRAGGSC  59Hajitou et al., TCM 16: 80-88 (2006) CKGGRAKDC  60Hajitou et al., TCM 16: 80-88 (2006) CVPELGHEC  61Hajitou et al., TCM 16: 80-88 (2006) CRRETAWAK  62Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) VSWFSHRYSPFAV  63Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) S GYRDGYAGPILYN  64Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) XXXY*XXX  65Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) Y*E/MNW  66Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) RPLPPLP  67Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) APPLPPR  68Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) DVFYPYPYASGS  69Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) MYWYPY  70Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) DITWDQLWDLMK  71Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) CWDD(G/L)WLC  72Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) EWCEYLGGYLRCY  73Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) A YXCXXGPXTWXCX  74Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) P IEGPTLRQWLAARA  75Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) LWXX(Y/W/F/H)  76Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) XFXXYLW  77Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) RWGLCD  78Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) MSRPACPPNDKYE  79Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) CLRSGRGC  80Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) CHWMFSPWC  81Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) WXXF  82Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) CSSRLDAC  83Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) CLPVASC  84Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) CGFECVRQCPERC  85Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) CVALCREACGEGC  86Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) SWCEPGWCR  87Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) YSGWGW  88Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) GLSGGRS  89Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) LMLPRAD  90Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) CSCFRDVCC  91Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) CRDVVSVIC  92Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) CNGRC  93Koivunen et al., J. Nucl. Med. 40: 883-888 (1999) MARSGL  94Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) MARAKE  95Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) MSRTMS  96Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) KCCYSL  97Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) MYWGDSHWLQYW  98Newton & Deutscher, Phage Peptide Display in YEHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) MQLPLAT  99Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) EWLS 100Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) SNEW 101Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) TNYL 102Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) WIFPWIQL 103Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) WDLAWMFRLPVG 104Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) CTVALPGGYVRVC 105Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) CVPELGHEC 106Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) CGRRAGGSC 107Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) CVAYCIEHHCWTC 108Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) CVFAHNYDYLVC 109Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) CVFTSNYAFC 110Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) VHSPNKK 111Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) CDCRGDCFC 112Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) CRGDGWC 113Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) XRGCDX 114Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) PXX(S/T) 115Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) CTTHWGFTLC 116Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) SGKGPRQITAL 117Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) A(A/Q)(N/A)(L/Y) 118Newton & Deutscher, Phage Peptide Display in (T/V/M/R)(R/K)Handbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) VYMSPF 119Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) MQLPLAT 120Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) ATWLPPR 121Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) HTMYYHHYQHHL 122Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) SEVGCRAGPLQWL 123Newton & Deutscher, Phage Peptide Display in CEKYFGHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) CGLLPVGRPDRNV 124Newton & Deutscher, Phage Peptide Display in WRWLCHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) CKGQCDRFKGLPW 125Newton & Deutscher, Phage Peptide Display in ECHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) SGRSA 126Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) WGFP 127Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) LWXXAr 128Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) XFXXYLW 129Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) AEPMPHSLNFSQYL 130Newton & Deutscher, Phage Peptide Display in WYTHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) WAY(W/F)SP 131Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) IELLQAR 132Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) DITWDQLWDLMK 133Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) AYTKCSRQWRTCM 134Newton & Deutscher, Phage Peptide Display in TTHHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) PQNSKIPGPTFLDP 135Newton & Deutscher, Phage Peptide Display in HHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) SMEPALPDWWWK 136Newton & Deutscher, Phage Peptide Display in MFKHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) ANTPCGPYTHDCP 137Newton & Deutscher, Phage Peptide Display in VKRHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) TACHQHVRMVRP 138Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) VPWMEPAYQRFL 139Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) DPRATPGS 140Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) FRPNRAQDYNTN 141Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) CTKNSYLMC 142Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) C(R/Q)L/RT(G/N)XX 143Newton & Deutscher, Phage Peptide Display in G(A/V)GCHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) CPIEDRPMC 144Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) HEWSYLAPYPWF 145Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) MCPKHPLGC 146Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) RMWPSSTVNLSAG 147Newton & Deutscher, Phage Peptide Display in RRHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) SAKTAVSQRVWLP 148Newton & Deutscher, Phage Peptide Display in SHRGGEPHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) KSREHVNNSACPS 149Newton & Deutscher, Phage Peptide Display in KRITAALHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) EGFR 150Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) AGLGVR 151Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) GTRQGHTMRLGVS 152Newton & Deutscher, Phage Peptide Display in DGHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) IAGLATPGWSHWLA 153Newton & Deutscher, Phage Peptide Display in LHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) SMSIARL 154Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) HTFEPGV 155Newton & Deutscher, Phage Peptide Display inHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) NTSLKRISNKR1RR 156Newton & Deutscher, Phage Peptide Display in KHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) LRIKRKRRKRKKTR 157Newton & Deutscher, Phage Peptide Display in KHandbook of Experimental Pharmacology, pages145-163, Springer-Verlag, Berlin (2008) Y* is phospho-Tyr

In some embodiments, the targeting sequence may be a peptide that can beused for chemical coupling (e.g., can comprise arginine and/or lysineresidues that can be chemically coupled through their R groups) toanother molecule that targets entry into a cell.

In some embodiments, the AAV capsid protein subunit or protein capsidcan comprise a mutation as described in WO 2006/066066. For example, thecapsid protein subunit can comprise a selective amino acid substitutionat amino acid position 263, 705, 708 and/or 716 of the native AAV2capsid protein subunit or a corresponding change(s) in a capsid proteinsubunit from another AAV serotype.

Additionally, or alternatively, in some embodiments, the capsid proteinsubunit, protein capsid or viral vector comprises a selective amino acidinsertion directly following amino acid position 264 of the AAV2 capsidprotein subunit or a corresponding change in the capsid protein subunitfrom other AAV. By “directly following amino acid position X” it isintended that the insertion immediately follows the indicated amino acidposition (for example, “following amino acid position 264” indicates apoint insertion at position 265 or a larger insertion, e.g., frompositions 265 to 268, etc.).

Furthermore, in some embodiments, the capsid protein subunit, proteincapsid or viral vector can comprise amino acid modifications such asdescribed in PCT Publication No. WO 2010/093784 (e.g., 2i8) and/or inPCT Publication No. WO 2014/144229 (e.g., dual glycan).

In some embodiments, the capsid protein subunit, protein capsid or viralvector can have equivalent or enhanced transduction efficiency relativeto the transduction efficiency of the AAV serotype from which the capsidprotein subunit, protein capsid or viral vector originated. In someembodiments, the capsid protein subunit, protein capsid or viral vectorcan have reduced transduction efficiency relative to the transductionefficiency of the AAV serotype from which the capsid protein subunit,protein capsid or viral vector originated. In some embodiments, thecapsid protein subunit, protein capsid or viral vector can haveequivalent or enhanced tropism relative to the tropism of the AAVserotype from which the capsid protein subunit, protein capsid or viralvector originated. In some embodiments, the capsid protein subunit,protein capsid or viral vector can have an altered or different tropismrelative to the tropism of the AAV serotype from which the capsidprotein subunit, protein capsid or viral vector originated. In someembodiments, the capsid protein subunit, protein capsid or viral vectorcan have or be engineered to have tropism for brain tissue. In someembodiments, the capsid protein subunit, protein capsid or viral vectorcan have or be engineered to have tropism for liver tissue.

The AAV vectors described herein can be used to deliver a heterologousnucleic acid to a cell or subject. For example, the modified vector canbe used to treat a lysosomal storage disorder such as amucopolysaccharidosis disorder (e.g., Sly syndrome [3-glucuronidase],Hurler Syndrome [alpha-L-iduronidase], Scheie Syndrome[alpha-L-iduronidase], Hurler-Scheie Syndrome [alpha-L-iduronidase],Hunter's Syndrome [iduronate sulfatase], Sanfilippo Syndrome (A [heparansulfamidase], B [N-acetylglucosaminidase], C[acetyl-CoA:alpha-glucosaminide acetyltransferase], D[N-acetylglucosamine 6-sulfatase]), Morquio Syndrome (A[galactose-6-sulfate sulfatase], B [3-galactosidase]), Maroteaux-LamySyndrome [N-acetylgalactosamine-4-sulfatase], etc.), Fabry disease(a-galactosidase), Gaucher's disease (glucocerebrosidase), or a glycogenstorage disorder (e.g., Pompe disease; lysosomal acid alpha-glucosidase)as described herein.

Those skilled in the art will appreciate that for some AAV capsidprotein subunits, the corresponding modification will be an insertionand/or a substitution, depending on whether the corresponding amino acidpositions are partially or completely present in the virus or,alternatively, are completely absent.

In some embodiments, virus vectors comprise the modified capsid proteinsubunits and protein capsids described herein. In some embodiments, thevirus vector is a parvovirus vector (e.g., comprising a parvovirusprotein capsid and/or vector genome), for example, an AAV vector (e.g.,comprising an AAV protein capsid and/or vector genome). In someembodiments, the virus vector comprises a modified AAV protein capsidcomprising a modified capsid protein subunit as described herein and avector genome.

For example, in some embodiments, the virus vector comprises: (a) amodified protein capsid (e.g., a modified AAV protein capsid) comprisinga modified capsid protein subunit described herein; and (b) a nucleicacid comprising a terminal repeat sequence (e.g., an AAV TR), whereinthe nucleic acid comprising the terminal repeat sequence is encapsidatedby the modified protein capsid. The nucleic acid can optionally comprisetwo terminal repeats (e.g., two AAV TRs).

In some embodiments, the virus vector is a recombinant virus vectorcomprising a heterologous nucleic acid encoding a polypeptide orfunctional RNA of interest. Recombinant virus vectors are described inmore detail below.

In some embodiments, the virus vectors (i) have reduced transduction ofliver as compared with the level of transduction by a virus vectorwithout the modified capsid protein subunit; (ii) exhibit enhancedsystemic transduction by the virus vector in an animal subject ascompared with the level observed by a virus vector without the modifiedcapsid protein subunit; (iii) demonstrate enhanced movement acrossendothelial cells as compared with the level of movement by a virusvector without the modified capsid protein subunit, and/or (iv) exhibita selective enhancement in transduction of muscle tissue (e.g., skeletalmuscle, cardiac muscle and/or diaphragm muscle), (v) exhibit a selectiveenhancement in transduction of liver tissue, and/or (vi) reducedtransduction of brain tissues (e.g., neurons) as compared with the levelof transduction by a virus vector without the modified capsid proteinsubunit. In some embodiments, the virus vector has systemic transductiontoward liver.

In some embodiments, an adeno-associated virus (AAV) vector comprises:(i) a protein capsid comprising a capsid protein subunit comprising thesequence of SEQ ID NO: 180 or 175; and (ii) a transfer cassetteencapsidated by the protein capsid; wherein the transfer cassettecomprises from 5′ to 3′: a 5′ inverted terminal repeat (ITR); apromoter; a transgene which encodes the NPC1 protein; a polyadenylationsignal; and a 3′ ITR. In some embodiments, the capsid protein subunitcomprises the sequence of SEQ ID NO: 180. In some embodiments, thecapsid protein subunit comprises the sequence of SEQ ID NO: 175.

In some embodiments, an adeno-associated virus (AAV) vector comprises:(i) a protein capsid comprising a capsid protein subunit comprising thesequence of SEQ ID NO: 180 or 175, or a sequence comprising about 1 toabout 25 amino acid mutations relative to SEQ ID NO: 180 or 175; and(ii) a transfer cassette encapsidated by the protein capsid; wherein thetransfer cassette comprises from 5′ to 3′:a 5′ inverted terminal repeat(ITR); a promoter; a transgene which encodes the NPC1 protein; apolyadenylation signal; and a 3′ ITR. In some embodiments, the capsidprotein subunit comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more amino acid mutationsrelative to SEQ ID NO: 180 or 175.

In some embodiments, at least one of the 5′ ITR and the 3′ ITR is about110 to about 160 nucleotides in length. In some embodiments, the 5′ ITRis the same length as the 3′ ITR. In some embodiments the 5′ ITR and the3′ ITR have different lengths. In some embodiments, at least one of the5′ ITR and the 3′ ITR is isolated or derived from the genome of AAV1,AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12,AAVrh8, AAVrh10, AAVrh32.33, AAVrh74, Avian AAV or Bovine AAV. In someembodiments, the 5′ ITR comprises the sequence of SEQ ID NO: 3003. Insome embodiments, the 3′ ITR comprises the sequence of SEQ ID NO: 3004.

In some embodiments, the promoter is a constitutive promoter. In someembodiments, the promoter is an inducible promoter. In some embodiments,the promoter is a tissue-specific promoter. In some embodiments, thepromoter is selected from the group consisting of the CBA promoter, theGUSB240 promoter, the GUSB379 promoter, the HSVTK promoter, the CMVpromoter, the SV40 early promoter, the SV40 late promoter, themetallothionein promoter, the murine mammary tumor virus (MMTV)promoter, the Rous sarcoma virus (RSV) promoter, the polyhedrinpromoter, the chicken β-actin (CBA) promoter, the EF-1 alpha promoter,the dihydrofolate reductase (DHFR) promoter, and the phosphoglycerolkinase (PGK) promoter. In some embodiments, the promoter is selectedfrom the group consisting of the CBA promoter, the GUSB240 promoter, theGUSB379 promoter, and the HSVTK promoter. In some embodiments, thepromoter comprises a sequence at least 95% or 100% identical to any oneof SEQ ID NO: 3005, SEQ ID NO: 3006, SEQ ID NO: 3007, or SEQ ID NO:3008.

In some embodiments, the NPC1 protein is the human NPC1 protein. In someembodiments, the NPC1 protein has a sequence that is at least 90%identical to the sequence of the human NPC1 protein. In someembodiments, the NPC1 protein has a sequence that is at least 95%identical to the sequence of the human NPC1 protein. In someembodiments, the NPC1 protein has a sequence that is at least 98%identical to the sequence of the human NPC1 protein. In someembodiments, the NPC1 protein comprises the sequence of SEQ ID NO: 3001.

In some embodiments, the transgene comprises the sequence of SEQ ID NO:3002.

In some embodiments, the polyadenylation signal is selected from simianvirus 40 (SV40), rBG, α-globin, β-globin, human collagen, human growthhormone (hGH), polyoma virus, human growth hormone (hGH) and bovinegrowth hormone (bGH). In some embodiments, the polyadenylation signal isthe SV40 polyadenylation signal. In some embodiments, thepolyadenylation signal is the rBG polyadenylation signal.

In some embodiments, the polyadenylation signal comprises the sequenceat least 95% or 100% identical to SEQ ID NO: 3012 or to SEQ ID NO: 3013.

In some embodiments, the transfer cassette further comprises anenhancer. In some embodiments, the enhancer is the CMV enhancer. In someembodiments, the enhancer comprises the sequence of SEQ ID NO: 3009, ora sequence at least 95% identical thereto.

In some embodiments, the transfer cassette further comprises an intronicsequence. In some embodiments, the intronic sequence is a chimericsequence.

In some embodiments, the intronic sequence is a hybrid sequence. In someembodiments, the intronic sequence comprises a sequence isolated orderived from SV40. In some embodiments, the intronic sequence comprisesthe sequence of any one of SEQ ID NO: 3010-3011. In some embodiments,the AAV transfer cassette comprises the sequence of any one of SEQ IDNO: 3014-3019.

It will be understood by those skilled in the art that the modifiedcapsid protein subunits, protein capsids and virus vectors describedherein exclude those capsid protein subunits, protein capsids and virusvectors that have the indicated amino acids at the specified positionsin their native state (i.e., are not mutants).

AAV Transfer Cassettes

Described herein are AAV transfer cassettes, nucleic acids and plasmidsused in the production of recombinant adeno-associated viral (rAAV)vectors. The disclosed cassettes, nucleic acids and plasmids comprisesequences that may be used to express one or more transgenes havingtherapeutic efficacy in the amelioration, treatment and/or prevention ofone or more diseases or disorders.

In some embodiments, the AAV transfer cassettes comprise a 5′ invertedterminal repeat (ITR); a transgene; and a 3′ ITR. In some embodiments,the AAV transfer cassettes comprise a 5′ ITR, a promoter, a transgene,and a 3′ ITR. In some embodiments, the AAV transfer cassettes comprise a5′ ITR, a promoter, a transgene, a polyadenylation sequence and a 3′ITR. In some embodiments, the AAV transfer cassettes comprise a 5′ ITR,a promoter, a transgene, a polyadenylation sequence and a 3′ ITR;wherein the transfer cassette comprises an intronic sequence. In someembodiments, the AAV transfer cassettes comprise a 5′ ITR, a promoter,an intronic sequence, a transgene, a polyadenylation sequence and a 3′ITR. In some embodiments, wherein the transgene encodes the NPC1protein, or a fragment or variant thereof.

Inverted Terminal Repeat

Inverted Terminal Repeat or ITR sequences are sequences that mediate AAVproviral integration and for packaging of AAV DNA into virions. ITRs areinvolved in a variety of activities in the AAV life cycle. For example,the ITR sequences, which can form a hairpin structure, play roles inexcision from the plasmid after transfection, replication of the vectorgenome, and integration and rescue from a host cell genome.

The AAV transfer cassettes of the disclosure may comprise a 5′ ITR and a3′ ITR. The ITR sequences may be about 110 to about 160 nucleotides inlength, for example 110, 111, 112, 113, 114, 115, 116, 117, 118, 119,120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133,134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147,148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159 or 160nucleotides in length. In some embodiments, the ITR sequences may beabout 141 nucleotides in length. In some embodiments, the 5′ ITR is thesame length as the 3′ ITR. In some embodiments, the 5′ ITR and the 3′ITR have different lengths. In some embodiments, the 5′ ITR is longerthan the 3′ ITR, and in other embodiments, the 3′ ITR is longer than the5′ ITR.

The ITRs may be isolated or derived from the genome of any AAV, forexample the AAVs listed in Table 1. In some embodiments, at least one ofthe 5′ ITR and the 3′ ITR is isolated or derived from the genome ofAAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11,AAV12, AAVrh8, AAVrh10, AAVrh32.33, AAVrh74, Avian AAV or Bovine AAV. Insome embodiments, at least one of the 5′ ITR and the 3′ITR may be awildtype or mutated ITR isolated derived from a member of anotherparvovirus species besides AAV. For example, in some embodiments, an ITRmay be a wildtype or mutant ITR isolated or derived from bocavirus orparvovirus B19.

In some embodiments, the ITR comprises a modification to promoteproduction of a scAAV. In some embodiments, the modification to promoteproduction of a scAAV is deletion of the terminal resolution sequence(TRS) from the ITR. In some embodiments, the 5′ ITR is a wildtype ITR,and the 3′ ITR is a mutated ITR lacking the terminal resolutionsequence. In some embodiments, the 3′ ITR is a wildtype ITR, and the 5′ITR is a mutated ITR lacking the terminal resolution sequence. In someembodiments, the terminal resolution sequence is absent from both the 5′ITR and the 3′ITR. In other embodiments, the modification to promoteproduction of a scAAV is replacement of an ITR with a differenthairpin-forming sequence, such as a shRNA-forming sequence.

In some embodiments, the 5′ ITR may comprise the sequence of SEQ ID NO:3003, or a sequence at least 95% identical thereto. In some embodiments,the 3′ ITR may comprise the sequence of SEQ ID NO: 3004, or a sequenceat least 95% identical thereto. In some embodiments, the 5′ ITRcomprises the sequence of SEQ ID NO: 3003, and the 3′ ITR comprises thesequence of SEQ ID NO: 3004.

In some embodiments, the AAV transfer cassettes comprise one or more“surrogate” ITRs, i.e., non-ITR sequences that serve the same functionas ITRs. See, e.g., Xie, J. et al., Mol. Ther., 25(6): 1363-1374 (2017).In some embodiments, an ITR in an AAV transfer cassette is replaced by asurrogate ITR. In some embodiments, the surrogate ITR comprises ahairpin-forming sequence. In some embodiments, the surrogate ITR is ashort hairpin (sh)RNA-forming sequence.

Promoters, Enhancers, Repressors and Other Regulatory Sequences

Gene expression may be controlled by nucleotide sequences calledpromoters and enhancers that flank the coding region for a givenprotein.

As used herein, the term “promoter” refers to one or more nucleic acidcontrol sequences that direct transcription of an operably linkednucleic acid. Promoters may include nucleic acid sequences near thestart site of transcription, such as a TATA element. Promoters may alsoinclude cis-acting polynucleotide sequences that can be bound bytranscription factors.

A “constitutive” promoter is a promoter that is active under mostenvironmental and developmental conditions. An “inducible” promoter is apromoter that is active under environmental or developmental regulation.The term “operably linked” refers to a functional linkage between anucleic acid expression control sequence (such as a promoter, or arrayof transcription factor binding sites) and a second nucleic acidsequence, wherein the expression control sequence directs transcriptionof the nucleic acid corresponding to the second sequence.

Gene expression may also be controlled by one or more distal “enhancer”or “repressor” elements, which can be located as much as severalthousand base pairs from the start site of transcription. Enhancer orrepressor elements regulate transcription in an analogous manner tocis-acting elements near the start site of transcription, with theexception that enhancer elements can act from a distance from the startsite of transcription.

In some embodiments, the AAV transfer cassettes described hereincomprise a promoter. They promoter may be, for example, a constitutivepromoter or an inducible promoter. In some embodiments, the promoter isa tissue-specific promoter.

Exemplary promoters that may be used in the AAV transfer cassettesdescribed herein include the CMV promoter, the SV40 early promoter, theSV40 late promoter, the metallothionein promoter, the murine mammarytumor virus (MMTV) promoter, the Rous sarcoma virus (RSV) promoter, thepolyhedrin promoter, the chicken p-actin (CBA) promoter, thedihydrofolate reductase (DHFR) promoter, and the phosphoglycerol kinase(PGK) promoter. In some embodiments, the promoter is selected from thegroup consisting of the chicken p-actin (CBA) promoter the EF-1 alphapromoter, and the EF-1 alpha short promoter. In some embodiments, thepromoter comprises a sequence selected from any one of SEQ ID NO:3005-3008, or a sequence at least 95% identical thereto.

In some embodiments, the AAV transfer cassettes described hereincomprise an enhancer. The enhancer may be, for example, the CMVenhancer. In some embodiments, the enhancer comprises the sequence ofSEQ ID NO: 3009, or a sequence at least 95% identical thereto.

A non-limiting list of exemplary tissue-specific promoters and enhancersthat may be used in the AAV transfer cassettes described hereinincludes: HMG-COA reductase promoter; sterol regulatory element 1(SRE-1); phosphoenol pyruvate carboxy kinase (PEPCK) promoter; humanC-reactive protein (CRP) promoter; human glucokinase promoter;cholesterol 7-alpha hydroylase (CYP-7) promoter; beta-galactosidasealpha-2,6 sialyltransferase promoter; insulin-like growth factor bindingprotein (IGFBP-1) promoter; aldolase B promoter; human transferrinpromoter; collagen type I promoter; prostatic acid phosphatase (PAP)promoter; prostatic secretory protein of 94 (PSP 94) promoter; prostatespecific antigen complex promoter; human glandular kallikrein genepromoter (hgt-1); the myocyte-specific enhancer binding factor MEF-2;muscle creatine kinase promoter; pancreatitis associated proteinpromoter (PAP); elastase 1 transcriptional enhancer; pancreas specificamylase and elastase enhancer promoter; pancreatic cholesterol esterasegene promoter; uteroglobin promoter; cholesterol side-chain cleavage(SCC) promoter; gamma-gamma enolase (neuron-specific enolase, NSE)promoter; neurofilament heavy chain (NF-H) promoter; humanCGL-1/granzyme B promoter; the terminal deoxy transferase (TdT), lambda5, VpreB, and Ick (lymphocyte specific tyrosine protein kinase p561ck)promoter; the humans CD2 promoter and its 3′ transcriptional enhancer;the human NK and T cell specific activation (NKG5) promoter; pp60c-srctyrosine kinase promoter; organ-specific neoantigens (OSNs), mw 40 kDa(p40) promoter; colon specific antigen-P promoter; humanalpha-lactalbumin promoter; phosphoeholpyruvate carboxykinase (PEPCK)promoter, HER2/neu promoter, casein promoter, IgG promoter, ChorionicEmbryonic Antigen promoter, elastase promoter, porphobilinogen deaminasepromoter, insulin promoter, growth hormone factor promoter, tyrosinehydroxylase promoter, albumin promoter, alphafetoprotein promoter,acetyl-choline receptor promoter, alcohol dehydrogenase promoter, alphaor beta globin promoter, T-cell receptor promoter, the osteocalcinpromoter the IL-2 promoter, IL-2 receptor promoter, whey (wap) promoter,and the MHC Class II promoter.

Transene

The AAV transfer cassettes described herein comprise a transgene forexpression in a target cell.

The transgene may be any heterologous nucleic acid sequence(s) ofinterest. Such nucleic acids may include nucleic acids encodingpolypeptides, including therapeutic (e.g., for medical or veterinaryuses) or immunogenic (e.g., for vaccines) polypeptides or RNAs.Alternatively, the nucleic acid may encode an antisense nucleic acid, aribozyme, RNAs that effect spliceosome-mediated/ram-splicing,interfering RNAs (RNAi) including siRNA, shRNA or miRNA that mediategene silencing, and other non-translated RNAs. In some embodiments, thenucleic acid sequence may direct gene editing. For example, the nucleicacid may encode a gene-editing molecule such as a guide RNA or anuclease. In some embodiments, the nucleic acid may encode a zinc-fingernuclease, a homing endonuclease, a TALEN (transcription activator-likeeffector nuclease), a NgAgo (agronaute endonuclease), a SGN(structure-guided endonuclease), or a RGN (RNA-guided nuclease) such asa Cas9 nuclease or a Cpf1 nuclease. In some embodiments, the nucleicacid may share homology with and recombine with a locus on a hostchromosome. This approach can be utilized, for example, to correct agenetic defect in the host cell.

The virus vectors according to the present disclosure provide a meansfor delivering transgenes into a broad range of cells, includingdividing and non-dividing cells. The virus vectors can be employed todeliver a transgene to a cell in vitro, e.g., to produce a polypeptidein vitro or for ex vivo gene therapy. The virus vectors are additionallyuseful in a method of delivering a transgene to a subject in needthereof, e.g., to express an immunogenic or therapeutic polypeptide or afunctional RNA. In this manner, the polypeptide or functional RNA can beproduced in vivo in the subject. The subject can be in need of thepolypeptide because the subject has a deficiency of the polypeptide.Further, the method can be practiced because the production of thepolypeptide or functional RNA in the subject may impart some beneficialeffect. As used herein, the term “functional RNA” refers to anynon-coding RNA sequence that has one or more functions in a cell, suchas those described in the preceding paragraph.

The virus vectors can also be used to deliver nucleic acids for theproduction of a polypeptide of interest or functional RNA in culturedcells or in a subject (e.g., using the subject as a bioreactor toproduce the polypeptide or to observe the effects of the functional RNAon the subject, for example, in connection with screening methods).

In general, the virus vectors of the present disclosure can be employedto deliver a transgene encoding a polypeptide or functional RNA to treatand/or prevent any disease state for which it is beneficial to deliver atherapeutic polypeptide or functional RNA.

In some embodiments, the transgene is useful for treating NPC1. In someembodiments, the transgene encodes the NPC1 protein. The NPC1 proteinmay be, for example, the human NPC1 protein. In some embodiments, theNPC1 protein has a sequence that is at least 90% identical, at least 95%identical, or at least 98% identical to the sequence of the human NPC1protein. In some embodiments, the NPC1 protein comprises one or more ofthe single nucleotide changes listed in the Table 9 (numbering based onSEQ ID NO: 3001 or 3020). In some embodiments, the NPC1 protein is atruncated form of the human NPC1 protein. In some embodiments, the NPC1protein comprises the sequence of SEQ ID NO: 3001, or a sequence atleast 90% identical, at least 95% identical, at least 96% identical, atleast 97% identical, at least 98% identical, or at least 99% identicalthereto. In some embodiments, the NPC1 protein comprises the sequence ofSEQ ID NO: 3020, or a sequence at least 90% identical, at least 95%identical, at least 96% identical, at least 97% identical, at least 98%identical, or at least 99% identical thereto. In some embodiments, theNPC1 protein comprises the sequence of SEQ ID NO: 3001 or 3020, with oneor more of the single nucleotide changes listed in Table 9. In someembodiments, the NPC1 protein has a sequence as shown in UniProtAccession No. 015118, incorporated herein by reference in its entirety.

In some embodiments, the transgene comprises the sequence of SEQ ID NO:3002, or a sequence at least 90% identical, at least 95% identical, atleast 96% identical, at least 97% identical, at least 98% identical, orat least 99% identical thereto. In some embodiments, the transgenecomprises the sequence of SEQ ID NO: 3002, or a sequence with 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, or more nucleic acid changes relativethereto. In some embodiments, the transgene encodes the amino acidsequence of SEQ ID NO: 3001. In some embodiments, the transgene encodesthe amino acid sequence of SEQ ID NO: 3020.

TABLE 9 NPC1 Variant Sequences Position numbering based on SEQ ID NO:3001 or SEQ ID NO: 3020. Position Mutation 63 C→R 74 C→Y 92 Q→R 113 C→R137 T→M 151 S→G 166 P→S 177 C→G 177 C→Y 215 H→R 222 N→S 231 V→G 237 P→S242 D→H 242 D→N 247 C→Y 248 G→V 272 M→R 333 G→D 372 R→W 378 V→A 380 L→F381 W→C 388 A→P 389 R→C 401 P→T 404 R→P 404 R→Q 404 R→W 433 P→L 434 P→L434 P→S 451 E→K 472 L→P 473 S→P 474 P→L 479 C→Y 509 Y→S 510 H→P 511 T→M512 H→R 518 R→Q 518 R→W 521 A→S 537 F→L 543 P→L 574 T→K 576 K→R 605 A→V612 E→D 615 R→C 615 R→L 631 M→R 640 G→R 642 M→I 652 S→W 660 G→S 664 V→M666 S→N 670 C→W 673 G→V 684 L→F 691 P→L 695 L→V 700 D→N 703 F→S 724 L→P727 V→F 734 S→I 742 E→K 745 A→E 754 M→K 757 V→A 763 F→L 767 A→V 775 Q→P789 R→C 789 R→G 825 Y→C 849 S→I 858 I→V 862 Q→L 865 S→L 871 Y→C 873 V→A874 D→V 888 P→S 889 V→M 890 Y→C 899 Y→D 910 G→S 917 D→Y 926 A→T 927 A→V928 Q→P 929 L→P 934 R→Q 940 S→L 942 W→C 943 I→M 944 D→N 945 D→N 948 D→H948 D→N 948 D→Y 950 V→M 954 S→L 956 C→Y 958 R→L 958 R→Q 959 V→E 961-966NITDQF→S 961 N→S 968 N→S 971 V→G 976 C→R 978 R→C 986 G→S 992 G→A 992 G→R992 G→W 996 M→R 1004 S→L 1007 P→A 1012 G→D 1015 G→V 1016 H→R 1023 V→G1034 G→R 1035 A→V 1036 T→K 1036 T→M 1049 A→V 1054 A→T 1059 R→Q 1061 I→T1062 A→V 1066 T→N 1087 F→L 1088 Y→C 1089 E→K 1094 I→T 1097 D→N 1137 N→I1140 G→V 1142 M→T 1150 N→K 1156 N→I 1156 N→S 1165 V→M 1167 F→L 1168 C→Y1174 A→V 1186 R→H 1189 E→G 1205 T→K 1205 T→R 1212 V→L 1213 L→F 1213 L→V1216 A→V 1220 I→T 1224 F→L 1236 G→E 1240 G→R 1249 S→G 1266 R→Q

Polyadenylation (PolyA) Signal

Polyadenylation signals are nucleotide sequences found in nearly allmammalian genes and control the addition of a string of approximately200 adenosine residues (the poly(A) tail) to the 3′ end of the genetranscript. The poly(A) tail contributes to mRNA stability, and mRNAslacking the poly(A) tail are rapidly degraded. There is also evidencethat the presence of the poly(A) tail positively contributes to thetranslatability of mRNA by affecting the initiation of translation.

In some embodiments, the AAV transfer cassettes of the disclosurecomprise a polyadenylation signal. The polyadenylation signal may beselected from the polyadenylation signal of simian virus 40 (SV40),α-globin, β-globin, human collagen, human growth hormone (hGH), polyomavirus, human growth hormone (hGH) and bovine growth hormone (bGH). Insome embodiments, the polyadenylation signal is the SV40 polyadenylationsignal. In some embodiments, the polyadenylation signal is the rBGpolyadenylation signal. In some embodiments, the polyadenylation signalcomprises the sequence of SEQ ID NO: 3012 or SEQ ID NO: 3013. In someembodiments, the polyadenylation signal comprises a sequence at least90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least99% identical to the sequence of SEQ ID NO: 3012 or SEQ ID NO: 3013.

Stuffer Sequences

AAV vectors typically accept inserts of DNA having a defined size rangewhich is generally about 4 kb to about 5.2 kb, or slightly more. Thus,for shorter transgene sequences, it may be necessary to includeadditional nucleic acid in the insert fragment in order to achieve therequired length which is acceptable for the AAV vector. Accordingly, insome embodiments, the AAV transfer cassettes of the disclosure maycomprise a suffer sequence. The stuffer sequence may be for example, asequence between 1-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-75, 75-100,100-150, 150-200, 200-250, 250-300, 300-400, 400-500, 500-750,750-1,000, 1,000-1,500, 1,500-2,000, 2,000-2,500, 2,500-3,000,3,000-3,500, 3,500-4,000, 4,000-4,500, to 4,500-5,000 nucleotides inlength. The stuffer sequence can be located in the cassette at anydesired position such that it does not prevent a function or activity ofthe vector.

Intronic Sequences

In some embodiments, the AAV transfer cassettes of the disclosure maycomprise an intronic sequence. Inclusion of an intronic sequence mayenhance expression compared with expression in the absence of theintronic sequence. In some the intronic sequence can increase geneexpression without functioning as a binding site for transcriptionfactors. For example, the intronic sequence can increase transcriptlevels by affecting the rate of transcription, nuclear export, andtranscript stability. In some embodiments, the intronic sequenceincreases the efficiency of mRNA translation.

In some embodiments, the intronic sequence is a hybrid or chimericsequence. In some embodiments, the intronic sequence is isolated orderived from an intronic sequence of one or more of SV40, β-globin,chicken beta-actin, minute virus of mice (MVM), factor IX, and/or humanIgG (heavy or light chain). In some embodiments, the intronic sequenceis isolated or derived from SV40. In some embodiments, the intronicsequence is chimeric. In some embodiments, the intronic sequencecomprises the sequence of SEQ ID NO: 3010 or SEQ ID NO:3011, or asequence that is at least 90%, at least 95%, at least 96%, at least 97%,at least 98%, or at least 99% identical thereto.

The intronic sequence may be located anywhere in the transfer cassettewhere it doesn't interfere with production of the AAV vector. Forexample, in some embodiments, the intronic sequence may be locatedbetween the promoter and the transgene.

Illustrative AAV Transfer Cassettes

In some embodiments, an adeno-associated virus (AAV) transfer cassettecomprises a 5′ inverted terminal repeat (ITR), a promoter, a transgene,a polyadenylation signal, and a 3′ ITR. In some embodiments, anadeno-associated virus (AAV) transfer cassette comprises a 5′ invertedterminal repeat (ITR), a promoter, an intronic sequence, a transgene, apolyadenylation signal, and a 3′ ITR. In some embodiments, the transgeneencodes the NPC1 protein. In some embodiments, the AAV transfer cassettefurther comprises an enhancer. In some embodiments, the AAV transfercassette further comprises an intronic sequence.

In some embodiments, the 5′ ITR comprises the sequence of SEQ ID NO:3003 and the 3′ ITR comprises the sequence of SEQ ID NO: 3004. In someembodiments, the enhancer comprises the sequence of SEQ ID NO: 3009. Insome embodiments, the promoter comprises the sequence of any one of SEQID NO: 3005-3008. In some embodiments, the intronic sequence comprisesthe sequence of SEQ ID NO: 3010 or 3011. In some embodiments, thetransgene comprises the sequence of SEQ ID NO: 3002. In someembodiments, the polyA signal comprises the sequence of SEQ ID NO: 3012or 3013. In some embodiments, the AAV transfer cassette comprises thesequence of any one of SEQ ID NO: 3014-3019.

In some embodiments, an AAV transfer cassette comprises a 5′ ITR, a CBApromoter, a SV40 intron, a transgene encoding the NPC1 protein, a SV40polyadenylation signal, and a 3′ ITR. In some embodiments, an AAVtransfer cassette comprises a 5′ ITR, a GUSB240 promoter, a chimericintron, a transgene encoding the NPC1 protein, a rBG polyadenylationsignal, and a 3′ ITR. In some embodiments, an AAV transfer cassettecomprises a 5′ ITR, a GUSB379 promoter, a SV40 intron, a transgeneencoding the NPC1 protein, a rBG polyadenylation signal, and a 3′ ITR.In some embodiments, an AAV transfer cassette comprises a 5′ ITR, aGUSB240 promoter, a chimeric intron, a transgene encoding the NPC1protein, a SV40 polyadenylation signal, and a 3′ ITR. In someembodiments, an AAV transfer cassette comprises a 5′ ITR, a GUSB240promoter, a SV40 intron, a transgene encoding the NPC1 protein, a SV40polyadenylation signal, and a 3′ ITR. In some embodiments, an AAVtransfer cassette comprises a 5′ ITR, a CMV enhancer, a HSVTK promoter,a transgene encoding the NPC1 protein, a rBG polyadenylation signal, anda 3′ ITR.

In some embodiments, an AAV transfer cassette comprises a 5′ ITRcomprising the sequence of SEQ ID NO: 3003, a CBA promoter comprisingthe sequence of SEQ ID NO: 3005, a SV40 intron comprising the sequenceof SEQ ID NO: 3010, a transgene encoding the NPC1 protein (SEQ ID NO:3001), a SV40 polyadenylation signal comprising SEQ ID NO: 3012, and a3′ ITR comprising the sequence of SEQ ID NO: 3004.

In some embodiments, an AAV transfer cassette comprises a 5′ ITRcomprising the sequence of SEQ ID NO: 3003, a GUSB240 promotercomprising the sequence of SEQ ID NO: 3006, a chimeric intron comprisingSEQ ID NO: 3011, a transgene encoding the NPC1 protein (SEQ ID NO:3001), a rBG polyadenylation signal comprising SEQ ID NO: 3013, and a 3′ITR comprising the sequence of SEQ ID NO: 3004.

In some embodiments, an AAV transfer cassette comprises a 5′ ITRcomprising the sequence of SEQ ID NO: 3003, a GUSB379 promotercomprising SEQ ID NO: 3006, a SV40 intron comprising the sequence of SEQID NO: 3010, a transgene encoding the NPC1 protein (SEQ ID NO: 3001), arBG polyadenylation signal comprising SEQ ID NO: 3013, and a 3′ ITRcomprising the sequence of SEQ ID NO: 3004.

In some embodiments, an AAV transfer cassette comprises a 5′ ITRcomprising the sequence of SEQ ID NO: 3003, a GUSB240 promotercomprising SEQ ID NO: 3007, a chimeric intron comprising the sequence ofSEQ ID NO: 3011, a transgene encoding the NPC1 protein (SEQ ID NO:3001), a SV40 polyadenylation signal comprising SEQ ID NO: 3012, and a3′ ITR comprising the sequence of SEQ ID NO: 3004.

In some embodiments, an AAV transfer cassette comprises a 5′ ITRcomprising the sequence of SEQ ID NO: 3003, a GUSB240 promotercomprising SEQ ID NO: 3006, a SV40 intron comprising the sequence of SEQID NO: 3010, a transgene encoding the NPC1 protein (SEQ ID NO: 3001), aSV40 polyadenylation signal comprising SEQ ID NO: 3012, and a 3′ ITRcomprising the sequence of SEQ ID NO: 3004.

In some embodiments, an AAV transfer cassette comprises a 5′ ITRcomprising the sequence of SEQ ID NO: 3003, a CMV enhancer, a HSVTKpromoter comprising SEQ ID NO: 3008, a transgene encoding the NPC1protein (SEQ ID NO: 3001), a rBG polyadenylation signal comprising SEQID NO: 3013, and a 3′ ITR comprising the sequence of SEQ ID NO: 3004.

In some embodiments, a nucleic acid comprises an AAV transfer cassette.In some embodiments, a nucleic acid comprises a transgene, wherein thetransgene encodes the amino acid sequence of SEQ ID NO: 3001. In someembodiments, a nucleic acid comprises a transgene, wherein the transgeneencodes the amino acid sequence of SEQ ID NO: 3020. In some embodiments,a nucleic acid comprises, from 5′ to 3′, a 5′ inverted terminal repeat(ITR); a promoter; a transgene; a polyadenylation signal; and a 3′ ITR;wherein the transgene encodes the amino acid sequence of SEQ ID NO: 3001or SEQ ID NO: 3020. In some embodiments, a nucleic acid comprises, from5′ to 3′, a 5′ inverted terminal repeat (ITR); a promoter; a transgene;a polyadenylation signal; and a 3′ ITR; wherein the nucleic acidcomprises an intronic sequence; wherein the transgene encodes the aminoacid sequence of SEQ ID NO: 3001 or SEQ ID NO: 3020. In someembodiments, a nucleic acid comprises, from 5′ to 3′, a 5′ invertedterminal repeat (ITR); a chicken beta-actin promoter; a transgene; apolyadenylation signal; and a 3′ ITR; wherein the transfer cassettecomprises an intronic sequence; wherein the transgene encodes the aminoacid sequence of SEQ ID NO: 3001 or SEQ ID NO: 3020. In someembodiments, a nucleic acid comprises, from 5′ to 3′, a 5′ invertedterminal repeat (ITR); a promoter; an intronic sequence; a transgene; apolyadenylation signal; and a 3′ ITR; wherein the transgene encodes theamino acid sequence of SEQ ID NO: 3001 or SEQ ID NO: 3020. In someembodiments, a nucleic acid comprises, from 5′ to 3′, a 5′ invertedterminal repeat (ITR); a chicken beta-actin promoter; an intronicsequence; a transgene; a polyadenylation signal; and a 3′ ITR; whereinthe transgene encodes the amino acid sequence of SEQ ID NO: 3001 or SEQID NO: 3020. The AAV transfer cassettes described herein may beincorporated into a vector (e.g., a plasmid or a bacmid) using standardmolecular biology techniques. The vector (e.g., plasmid or bacmid) mayfurther comprise one or more genetic elements used during production ofAAV, including, for example, AAV rep and cap genes, and helper virusprotein sequences.

Methods for Producing Virus Vectors

Also provided herein are methods of producing virus vectors. In someembodiments, a method of producing an AAV vector that evadesneutralizing antibodies, comprises: a) identifying contact amino acidresidues that form a three dimensional antigenic footprint on an AAVcapsid protein subunit or protein capsid; b) generating a library of AAVcapsid protein subunits comprising amino acid substitutions of thecontact amino acid residues identified in (a); c) producing AAVparticles comprising capsid protein subunits from the library of AAVcapsid protein subunits of (b); d) contacting the AAV particles of (c)with cells under conditions whereby infection and replication can occur;e) selecting AAV particles that can complete at least one infectiouscycle and replicate to titers similar to control AAV particles: 1)contacting the AAV particles selected in (e) with neutralizingantibodies and cells under conditions whereby infection and replicationcan occur; and g) selecting AAV particles that are not neutralized bythe neutralizing antibodies of (f). Nonlimiting examples of methods foridentifying contact amino acid residues include peptide epitope mappingand/or cryo-electron microscopy.

Resolution and identification of the antibody contact residues withinthe three dimensional antigenic footprint allows for their subsequentmodification through random, rational and/or degenerate mutagenesis togenerate antibody-evading AAV protein capsids and/or capsid proteinsubunits that can be identified through further selection and/orscreening.

Thus, in some embodiments, a method of producing an AAV vector thatevades neutralizing antibodies comprises: a) identifying contact aminoacid residues that form a three dimensional antigenic footprint on anAAV capsid protein subunits and/or protein capsids; b) generating AAVcapsid protein subunits comprising amino acid substitutions of thecontact amino acid residues identified in (a) by random, rational and/ordegenerate mutagenesis; c) producing AAV particles comprising capsidprotein subunits from the AAV capsid protein subunits of (b); d)contacting the AAV particles of (c) with cells under conditions wherebyinfection and replication can occur; e) selecting AAV particles that cancomplete at least one infectious cycle and replicate to titers similarto control AAV particles; f) contacting the AAV particles selected in(e) with neutralizing antibodies and cells under conditions wherebyinfection and replication can occur; and g) selecting AAV particles thatare not neutralized by the neutralizing antibodies of (f).

Nonlimiting examples of methods for identifying contact amino acidresidues include peptide epitope mapping and/or cryo-electronmicroscopy. Methods of generating AAV capsid protein subunits comprisingamino acid substitutions of contact amino acid residues by random,rational and/or degenerate mutagenesis are known in the art.

This comprehensive approach presents a platform technology that can beapplied to modifying any AAV protein capsid and/or capsid proteinsubunit. Application of this platform technology yields AAV antigenicvariants derived from the original AAV capsid protein subunit templatewithout loss of transduction efficiency. As one advantage and benefit,application of this technology will expand the cohort of patientseligible for gene therapy with AAV vectors.

In some embodiments, a method of producing a virus vector comprisesproviding to a cell: (a) a nucleic acid template comprising at least oneTR sequence (e.g., AAV TR sequence), and (b) AAV sequences sufficientfor replication of the nucleic acid template and encapsidation into AAVprotein capsids (e.g., AAV rep sequences and AAV cap sequences encodingthe AAV capsid subunits). Optionally, the nucleic acid template furthercomprises at least one heterologous nucleic acid sequence. In someembodiments, the nucleic acid template comprises two AAV ITR sequences,which are located 5′ and 3′ to the heterologous nucleic acid sequence(if present), although they need not be directly contiguous thereto.

The nucleic acid template and AAV rep and cap sequences are providedunder conditions such that virus vector comprising the nucleic acidtemplate packaged within the AAV protein capsid is produced in the cell.The method can further comprise the step of collecting the virus vectorfrom the cell. The virus vector can be collected from the medium and/orby lysing the cells.

The cell can be a cell that is permissive for AAV viral replication. Anysuitable cell known in the art may be employed. In some embodiments, thecell is a mammalian cell. As another option, the cell can be atrans-complementing packaging cell line that provides functions deletedfrom a replication-defective helper virus, e.g., 293 cells or other E1atrans-complementing cells.

The AAV replication and capsid protein subunit sequences may be providedby any method known in the art. Current protocols typically express theAAV rep/cap genes on a single plasmid. The AAV replication and packagingsequences need not be provided together, although it may be convenientto do so. The AAV rep and/or cap sequences may be provided by any viralor non-viral vector. For example, the rep/cap sequences may be providedby a hybrid adenovirus or herpesvirus vector (e.g., inserted into theE1a or E3 regions of a deleted adenovirus vector). EBV vectors may alsobe employed to express the AAV cap and rep genes. One advantage of thismethod is that EBV vectors are episomal, yet will maintain a high copynumber throughout successive cell divisions (i.e., are stably integratedinto the cell as extra-chromosomal elements, designated as an “EBV basednuclear episome,” see Margolski, (1992) Curr. Top. Microbiol. Immun.158:67).

As a further alternative, the rep/cap sequences may be stablyincorporated into a cell.

Typically the AAV rep/cap sequences will not be flanked by the TRs, toprevent rescue and/or packaging of these sequences.

The nucleic acid template can be provided to the cell using any methodknown in the art. For example, the template can be supplied by a plasmidor viral vector. In some embodiments, the nucleic acid template issupplied by a herpesvirus or adenovirus vector (e.g., inserted into theE1a or E3 regions of a deleted adenovirus). As another illustration,Palombo et al., (1998) J. Virology 72:5025, describes a baculovirusvector carrying a reporter gene flanked by the AAV TRs. EBV vectors mayalso be employed to deliver the template, as described above withrespect to the rep/cap genes.

In some embodiments, the nucleic acid template is provided by areplicating rAAV virus. In some embodiments, an AAV provirus comprisingthe nucleic acid template is stably integrated into the nucleus of thecell.

To enhance virus titers, helper virus functions (e.g., adenovirus orherpesvirus) that promote a productive AAV infection can be provided tothe cell. Helper virus sequences necessary for AAV replication are knownin the art. Typically, these sequences will be provided by a helperadenovirus or herpesvirus vector. Alternatively, the adenovirus orherpesvirus sequences can be provided by another non-viral or viralvector, e.g., as a noninfectious adenovirus miniplasmid that carries allof the helper genes that promote efficient AAV production as describedby Ferrari et al., (1997) Nature Med. 3: 1295, and U.S. Pat. Nos.6,040,183 and 6,093,570.

Further, the helper virus functions may be provided by a packaging cellwith the helper sequences embedded in the chromosome or maintained as astable extrachromosomal element. Generally, the helper virus sequencescannot be packaged into AAV virions, e.g., are not flanked by ITRs.

Those skilled in the art will appreciate that it may be advantageous toprovide the AAV replication and capsid protein subunit sequences and thehelper virus sequences (e.g., adenovirus sequences) on a single helperconstruct. This helper construct may be a non-viral or viral construct.As one nonlimiting illustration, the helper construct can be a hybridadenovirus or hybrid herpesvirus comprising the AAV rep/cap genes.

In some embodiments, the AAV rep/cap sequences and the adenovirus helpersequences are supplied by a single adenovirus helper vector. This vectorfurther can further comprise the nucleic acid template. The AAV rep/capsequences and/or the rAAV template can be inserted into a deleted region(e.g., the E1a or E3 regions) of the adenovirus.

In some embodiments, the AAV rep/cap sequences and the adenovirus helpersequences are supplied by a single adenovirus helper vector. Accordingto this embodiment, the rAAV template can be provided as a plasmidtemplate.

In some embodiments, the AAV rep/cap sequences and adenovirus helpersequences are provided by a single adenovirus helper vector, and therAAV template is integrated into the cell as a provirus. Alternatively,the rAAV template is provided by an EBV vector that is maintained withinthe cell as an extrachromosomal element (e.g., as an EBV based nuclearepisome).

In some embodiments, the AAV rep/cap sequences and adenovirus helpersequences are provided by a single adenovirus helper. The rAAV templatecan be provided as a separate replicating viral vector. For example, therAAV template can be provided by a rAAV particle or a second recombinantadenovirus particle.

According to the foregoing methods, the hybrid adenovirus vectortypically comprises the adenovirus 5′ and 3′ cis sequences sufficientfor adenovirus replication and packaging (i.e., the adenovirus terminalrepeats and PAC sequence). The AAV rep/cap sequences and, if present,the rAAV template are embedded in the adenovirus backbone and areflanked by the 5′ and 3′ cis sequences, so that these sequences may bepackaged into adenovirus protein capsids. As described above, theadenovirus helper sequences and the AAV rep/cap sequences are generallynot flanked by ITRs so that these sequences are not packaged into theAAV virions. Zhang et al., ((2001) Gene Ther. 18:704-12) describe achimeric helper comprising both adenovirus and the AAV rep and capgenes.

Herpesvirus may also be used as a helper virus in AAV packaging methods.Hybrid herpesviruses encoding the AAV Rep protein(s) may advantageouslyfacilitate scalable AAV vector production schemes. A hybrid herpessimplex virus type I (HSV-1) vector expressing the AAV-2 rep and capgenes has been described (Conway et al., (1999) Gene Therapy 6:986 andWO 00/17377.

As a further alternative, virus vectors can be produced in insect cellsusing baculovirus vectors to deliver the rep/cap genes and rAAV templateas described, for example, by Urabe et al., (2002) Human Gene Therapy13: 1935-43.

AAV vector stocks free of contaminating helper virus may be obtained byany method known in the art. For example, AAV and helper virus may bereadily differentiated based on size. AAV may also be separated awayfrom helper virus based on affinity for a heparin substrate (Zolotukhinet al. (1999) Gene Therapy 6:973). Deleted replication-defective helperviruses can be used so that any contaminating helper virus is notreplication competent. As a further alternative, an adenovirus helperlacking late gene expression may be employed, as only adenovirus earlygene expression is required to mediate packaging of AAV virus.Adenovirus mutants defective for late gene expression are known in theart (e.g., ts100K and ts149 adenovirus mutants).

Recombinant Virus Vectors

The virus vectors described herein are useful for the delivery ofnucleic acids to cells in vitro, ex vivo, and in vivo. In particular,the virus vectors can be advantageously employed to deliver or transfernucleic acids to animal, including mammalian, cells. Thus, in someembodiments, a nucleic acid may be encapsidated by a protein capsiddescribed herein. In some embodiments, the nucleic acid is a transfercassette. In some embodiments, the transfer cassette comprises a vectorgenome (e.g., 5′ ITR, transgene, and 3′ ITR). In some embodiments, thenucleic acid is an AAV transfer cassette.

The transfer cassette sequence delivered by the virus vectors may be anyheterologous nucleic acid sequence(s) of interest. Nucleic acids ofinterest include nucleic acids encoding polypeptides, includingtherapeutic (e.g., for medical or veterinary uses) or immunogenic (e.g.,for vaccines) polypeptides or RNAs. In some embodiments, the transfercassette comprises a 5′ ITR and a 3′ ITR. In some embodiments, thetransfer cassette comprises a 5′ ITR, a transgene, and a 3′ITR. In someembodiments, the transgene encodes a therapeutic protein or RNA.

Therapeutic polypeptides include, but are not limited to, cysticfibrosis transmembrane regulator protein (CFTR), dystrophin (includingmini- and micro-dystrophins, see, e.g., Vincent et al, (1993) NatureGenetics 5: 130; U.S. Patent Publication No. 2003/017131; Internationalpublication WO/2008/088895, Wang et al., Proc. Natl. Acad. Sci. USA 97:1 3714-13719 (2000); and Gregorevic et al., Mol. Ther. 16:657-64(2008)), myostatin propeptide, follistatin, activin type 11 solublereceptor, IGF-1, apolipoproteins such as apoA (apoA1, apoA2, apoA4,apoA-V), apoB (apoB100, ApoB48), apoC (apoCI, apoCII, apoCIII, apoCIV),apoD, apoE, apoH, apoL, apo(a), anti-inflammatory polypeptides such asthe Ikappa B dominant mutant, amyloid beta, tau, sarcospan, utrophin(Tinsley et al, (1996) Nature 384:349), mini-utrophin, clotting factors(e.g., Factor VIII, Factor IX, Factor X, etc.), erythropoietin,angiostatin, endostatin, catalase, tyrosine hydroxylase, superoxidedismutase, leptin, the LDL receptor, lipoprotein lipase, progranulin,ornithine transcarbamylase, β-globin, α-globin, spectrin,alpha-1-antitrypsin, adenosine deaminase, hypoxanthine guaninephosphoribosyl transferase, β-glucocerebrosidase, battenin,sphingomyelinase, lysosomal hexosaminidase A, branched-chain keto aciddehydrogenase, frataxin, RP65 protein, cytokines (e.g.,alpha-interferon, beta-interferon, gamma-interferon, interleukin-2,interleukin-4, alpha synuclein, parkin, granulocyte-macrophage colonystimulating factor, lymphotoxin, and the like), peptide growth factors,neurotrophic factors and hormones (e.g., somatotropin, insulin,insulin-like growth factors 1 and 2, platelet derived growth factor,epidermal growth factor, fibroblast growth factor, nerve growth factor,neurotrophic factor-3 and -4, brain-derived neurotrophic factor, bonemorphogenic proteins [including RANKL and VEGF], glial derived growthfactor, transforming growth factor-α and -β, and the like), huntingin,lysosomal acid alpha-glucosidase, iduronate-2-sulfatase,N-sulfoglucosamine sulfohydrolase, alpha-galactosidase A, receptors(e.g., the tumor necrosis growth factor soluble receptor), S100A1,ubiquitin protein ligase E3, parvalbumin, adenylyl cyclase type 6, amolecule that modulates calcium handling (e.g., SERCA_(2A), Inhibitor 1of PP1 and fragments thereof [e.g., WO 2006/029319 and WO 2007/100465]),a molecule that effects G-protein coupled receptor kinase type 2knockdown such as a truncated constitutively active bARKct,anti-inflammatory factors such as IRAP, anti-myostatin proteins,aspartoacylase, monoclonal antibodies (including single chain monoclonalantibodies; an exemplary Mab is the Herceptin® Mab), neuropeptides andfragments thereof (e.g., galanin, Neuropeptide Y (see, U.S. Pat. No.7,071,172)), angiogenesis inhibitors such as Vasohibins and other VEGFinhibitors (e.g., Vasohibin 2 [see, WO JP2006/073052]). Otherillustrative heterologous nucleic acid sequences encode suicide geneproducts (e.g., thymidine kinase, cytosine deaminase, diphtheria toxin,and tumor necrosis factor), proteins that enhance or inhibittranscription of host factors (e.g., nuclease-dead Cas9 linked to atranscription enhancer or inhibitor element, zinc-finger proteins linkedto a transcription enhancer or inhibitor element, transcriptionactivator-like (TAL) effectors linked to a transcription enhancer orinhibitor element), proteins conferring resistance to a drug used incancer therapy, tumor suppressor gene products (e.g., p53, Rb, Wt-1),TRAIL, FAS-ligand, and any other polypeptide that has a therapeuticeffect in a subject in need thereof. AAV vectors can also be used todeliver monoclonal antibodies and antibody fragments, for example, anantibody or antibody fragment directed against myostatin (see, e.g.,Fang et al., Nature Biotechnology 23:584-590 (2005)). Heterologousnucleic acid sequences encoding polypeptides include those encodingreporter polypeptides (e.g., an enzyme). Reporter polypeptides are knownin the art and include, but are not limited to, Green FluorescentProtein, β-galactosidase, alkaline phosphatase, luciferase, andchloramphenicol acetyltransferase gene.

Optionally, the heterologous nucleic acid encodes a secreted polypeptide(e.g., a polypeptide that is a secreted polypeptide in its native stateor that has been engineered to be secreted, for example, by operableassociation with a secretory signal sequence as is known in the art).

Alternatively, in some embodiments, the heterologous nucleic acid mayencode an antisense nucleic acid, a ribozyme (e.g., as described in U.S.Pat. No. 5,877,022), RNAs that effect spliceosome-mediated/ram-splicing(see, Puttaraju et al, (1999) Nature Biotech. 17:246; U.S. Pat. Nos.6,013,487; 6,083,702), interfering RNAs (RNAi) including siRNA, shRNA ormiRNA that mediate gene silencing (see, Sharp et al, (2000) Science287:2431), and other non-translated RNAs, such as “guide” RNAs (Gormanet al., (1998) Proc. Nat. Acad. Sci. USA 95:4929; U.S. Pat. No.5,869,248 to Yuan et al.), and the like. Exemplary untranslated RNAsinclude RNAi against a multiple drug resistance (MDR) gene product(e.g., to treat and/or prevent tumors and/or for administration to theheart to prevent damage by chemotherapy), RNAi against myostatin (e.g.,for Duchenne muscular dystrophy), RNAi against VEGF (e.g., to treatand/or prevent tumors), RNAi against phospholamban (e.g., to treatcardiovascular disease, see, e.g., Andino et al., J. Gene Med. 10:132-142 (2008) and Li et al., Acta Pharmacol Sin. 26:51-55 (2005));phospholamban inhibitory or dominant-negative molecules such asphospholamban S16E (e.g., to treat cardiovascular disease, see, e.g.,Hoshijima et al. Nat. Med. 8:864-871 (2002)), RNAi to adenosine kinase(e.g., for epilepsy), and RNAi directed against pathogenic organisms andviruses (e.g., hepatitis B and/or C virus, human immunodeficiency virus,CMV, herpes simplex virus, human papilloma virus, etc.).

Further, a nucleic acid sequence that directs alternative splicing canbe delivered. To illustrate, an antisense sequence (or other inhibitorysequence) complementary to the 5′ and/or 3′ splice site of dystrophinexon 51 can be delivered in conjunction with a U1 or U7 small nuclear(sn) RNA promoter to induce skipping of this exon. For example, a DNAsequence comprising a U1 or U7 snRNA promoter located 5′ to theantisense/inhibitory sequence(s) can be packaged and delivered in amodified protein capsid.

In some embodiments, a nucleic acid sequence that directs gene editingcan be delivered. For example, the nucleic acid may encode a guide RNA.In some embodiments, the guide RNA is a single guide RNA (sgRNA)comprising a crRNA sequence and a tracrRNA sequence. In someembodiments, the nucleic acid may encode a nuclease. In someembodiments, the nuclease is a zinc-finger nuclease, a homingendonuclease, a TALEN (transcription activator-like effector nuclease),a NgAgo (agronaute endonuclease), a SGN (structure-guided endonuclease),a RGN (RNA-guided nuclease), or modified or truncated variants thereof.In some embodiments, the RNA-guided nuclease is a Cas9 nuclease, aCas12(a) nuclease (Cpf1), a Cas12b nuclease, a Cas12c nuclease, aTrpB-like nuclease, a Cas13a nuclease (C2c2), a Cas13b nuclease, ormodified or truncated variants thereof. In some embodiments, the Cas9nuclease is isolated or derived from S. pyogenes or S. aureus.

In some embodiments, a nucleic acid sequence that directs gene knockdowncan be delivered. For example, the nucleic acid sequence may encode asiRNA, an shRNA, a microRNA, or an antisense nucleic acid. The virusvector may also comprise a heterologous nucleic acid that shareshomology with and recombines with a locus on a host chromosome. Thisapproach can be utilized, for example, to correct a genetic defect inthe host cell.

Also provided are virus vectors that express an immunogenic polypeptide,e.g., for vaccination. The nucleic acid may encode any immunogen ofinterest known in the art including, but not limited to, immunogens fromhuman immunodeficiency virus (HIV), simian immunodeficiency virus (SIV),influenza virus, HIV or SIV gag proteins, tumor antigens, cancerantigens, bacterial antigens, viral antigens, and the like.

The use of parvoviruses as vaccine vectors is known in the art (see,e.g., Miyamura el al, (1994) Proc. Nat. Acad. Sci USA 91:8507; U.S. Pat.No. 5,916,563 to Young et al, U.S. Pat. No. 5,905,040 to Mazzara et al,U.S. Pat. Nos. 5,882,652, 5,863,541 to Samulski et al). The antigen maybe presented in the parvovirus capsid.

Alternatively, the antigen may be expressed from a heterologous nucleicacid introduced into a recombinant vector genome. In some embodiments,any immunogen of interest as described herein and/or as is known in theart can be provided by the virus vectors described herein.

An immunogenic polypeptide can be any polypeptide suitable for elicitingan immune response and/or protecting the subject against an infectionand/or disease, including, but not limited to, microbial, bacterial,protozoal, parasitic, fungal and/or viral infections and diseases. Forexample, the immunogenic polypeptide can be an orthomyxovirus immunogen(e.g., an influenza virus immunogen, such as the influenza virushemagglutinin (HA) surface protein or the influenza virus nucleoprotein,or an equine influenza virus immunogen) or a lentivirus immunogen (e.g.,an equine infectious anemia virus immunogen, a Simian ImmunodeficiencyVirus (SIV) immunogen, or a Human Immunodeficiency Virus (HIV)immunogen, such as the HIV or SIV envelope GP 160 protein, the HIV orSIV matrix/capsid proteins, and the HIV or SIV gag, pol and env genesproducts). The immunogenic polypeptide can also be an arenavirusimmunogen (e.g., Lassa fever virus immunogen, such as the Lassa fevervirus nucleocapsid protein and the Lassa fever envelope glycoprotein), apoxvirus immunogen (e.g., a vaccinia virus immunogen, such as thevaccinia LI or L8 gene products), a flavivirus immunogen (e.g., a yellowfever virus immunogen or a Japanese encephalitis virus immunogen), afilovirus immunogen (e.g., an Ebola virus immunogen, or a Marburg virusimmunogen, such as NP and GP gene products), a bunyavirus immunogen(e.g., RVFV, CCHF, and/or SFS virus immunogens), or a coronavirusimmunogen (e.g., an infectious human coronavirus immunogen, such as thehuman coronavirus envelope glycoprotein, or a porcine transmissiblegastroenteritis virus immunogen, or an avian infectious bronchitis virusimmunogen). The immunogenic polypeptide can further be a polioimmunogen, a herpes immunogen (e.g., CMV, EBV, HSV immunogens), a mumpsimmunogen, a measles immunogen, a rubella immunogen, a diphtheria toxinor other diphtheria immunogen, a pertussis antigen, a hepatitis (e.g.,hepatitis A, hepatitis B, hepatitis C, etc.) immunogen, and/or any othervaccine immunogen now known in the art or later identified as animmunogen.

Alternatively, the immunogenic polypeptide can be any tumor or cancercell antigen. Optionally, the tumor or cancer antigen is expressed onthe surface of the cancer cell.

Exemplary cancer and tumor cell antigens are described in S. A.Rosenberg (Immunity 10:281 (1991)). Other illustrative cancer and tumorantigens include, but are not limited to: BRCA1 gene product, BRCA2 geneproduct, gp100, tyrosinase, GAGE-1/2, BAGE, RAGE, LAGE, NY-ESO-1, CDK-4,β-catenin, MUM-1, Caspase-8, KIAA0205, HPVE, SART-1, FRAME, p15,melanoma tumor antigens (Kawakami et al., (1994) Proc. Natl. Acad. Sci.USA 91:3515; Kawakami et al., (1994) J. Exp. Med., 180:347; Kawakami etal., (1994) Cancer Res. 54:3124), MART-1, gp100, MAGE-1, MAGE-2, MAGE-3,CEA, TRP-1, TRP-2, P-15, tyrosinase (Brichard et al., (1993) J Exp. Med.178:489); HER-2/neu gene product (U.S. Pat. No. 4,968,603), CA 125,LK26, FB5 (endosialin), TAG 72, AFP, CA 19-9, NSE, DU-PAN-2, CA50,SPan-1, CA72-4, HCG, STN (sialyl Tn antigen), c-erbB-2 proteins, PSA,L-CanAg, estrogen receptor, milk fat globulin, p53 tumor suppressorprotein (Levine, (1993) Ann. Rev. Biochem. 62:623); mucin antigens(International Patent Publication No. WO 90/05142); telomerases; nuclearmatrix proteins; prostatic acid phosphatase; papilloma virus antigens;and/or antigens now known or later discovered to be associated with thefollowing cancers: melanoma, adenocarcinoma, thymoma, lymphoma (e.g.,non-Hodgkin's lymphoma, Hodgkin's lymphoma), sarcoma, lung cancer, livercancer, colon cancer, leukemia, uterine cancer, breast cancer, prostatecancer, ovarian cancer, cervical cancer, bladder cancer, kidney cancer,pancreatic cancer, brain cancer and any other cancer or malignantcondition or metastasis thereof now known or later identified (see,e.g., Rosenberg, (1996) Ann. Rev. Med. 47:481-91).

As a further alternative, the heterologous nucleic acid can encode anypolypeptide that is desirably produced in a cell in vitro, ex vivo, orin vivo. For example, the virus vectors may be introduced into culturedcells and the expressed gene product isolated therefrom.

It will be understood by those skilled in the art that the heterologousnucleic acid(s) of interest can be operably associated with appropriatecontrol sequences. For example, the heterologous nucleic acid can beoperably associated with expression control elements, such astranscription/translation control signals, origins of replication,polyadenylation signals, internal ribosome entry sites (IRES),promoters, and/or enhancers, and the like.

Further, regulated expression of the heterologous nucleic acid(s) ofinterest can be achieved at the post-transcriptional level, e.g., byregulating selective splicing of different introns by the presence orabsence of an oligonucleotide, small molecule and/or other compound thatselectively blocks splicing activity at specific sites (e.g., asdescribed in WO 2006/119137).

Those skilled in the art will appreciate that a variety ofpromoter/enhancer elements can be used depending on the level andtissue-specific expression desired. The promoter/enhancer can beconstitutive or inducible, depending on the pattern of expressiondesired. The promoter/enhancer can be native or foreign and can be anatural or a synthetic sequence. By foreign, it is intended that thetranscriptional initiation region is not found in the wild-type hostinto which the transcriptional initiation region is introduced.

In some embodiments, the promoter/enhancer elements can be native to thetarget cell or subject to be treated. In some embodiments, thepromoters/enhancer element can be native to the heterologous nucleicacid sequence. The promoter/enhancer element is generally chosen so thatit functions in the target cell(s) of interest. Further, in someembodiments the promoter/enhancer element is a mammalianpromoter/enhancer element. The promoter/enhancer element may beconstitutive or inducible.

Inducible expression control elements are typically advantageous inthose applications in which it is desirable to provide regulation overexpression of the heterologous nucleic acid sequence(s). Induciblepromoters/enhancer elements for gene delivery can be tissue-specific or-preferred promoter/enhancer elements, and include muscle specific orpreferred (including cardiac, skeletal and/or smooth muscle specific orpreferred), neural tissue specific or preferred (includingbrain-specific or preferred), eye specific or preferred (includingretina-specific and cornea-specific), liver specific or preferred, bonemarrow specific or preferred, pancreatic specific or preferred, spleenspecific or preferred, and lung specific or preferred promoter/enhancerelements. Other inducible promoter/enhancer elements includehormone-inducible and metal-inducible elements. Exemplary induciblepromoters/enhancer elements include, but are not limited to, a Teton/off element, a RU486-inducible promoter, an ecdysone-induciblepromoter, a rapamycin-inducible promoter, and a metallothioneinpromoter.

In some embodiments wherein the heterologous nucleic acid sequence(s) istranscribed and then translated in the target cells, specific initiationsignals are generally included for efficient translation of insertedprotein coding sequences. These exogenous translational controlsequences, which may include the ATG initiation codon and adjacentsequences, can be of a variety of origins, both natural and synthetic.

The virus vectors described herein provide a means for deliveringheterologous nucleic acids into a broad range of cells, includingdividing and non-dividing cells. The virus vectors can be employed todeliver a nucleic acid of interest to a cell in vitro, e.g., to producea polypeptide in vitro or for ex vivo gene therapy. The virus vectorsare additionally useful in a method of delivering a nucleic acid to asubject in need thereof e.g., to express an immunogenic or therapeuticpolypeptide or a functional RNA. In this manner, the polypeptide orfunctional RNA can be produced in vivo in the subject. The subject canbe in need of the polypeptide because the subject has a deficiency ofthe polypeptide. Further, the method can be practiced because theproduction of the polypeptide or functional RNA in the subject mayimpart some beneficial effect.

The virus vectors can also be used to produce a polypeptide of interestor functional RNA in cultured cells or in a subject (e.g., using thesubject as a bioreactor to produce the polypeptide or to observe theeffects of the functional RNA on the subject, for example, in connectionwith screening methods).

In general, the virus vectors of the described herein can be employed todeliver a heterologous nucleic acid encoding a polypeptide or functionalRNA to treat and/or prevent any disease state for which it is beneficialto deliver a therapeutic polypeptide or functional RNA. Illustrativedisease states include, but are not limited to: cystic fibrosis (cysticfibrosis transmembrane regulator protein) and other diseases of thelung, hemophilia A (Factor VIII), hemophilia B (Factor IX), thalassemia(β-globin), anemia (erythropoietin) and other blood disorders.Alzheimer's disease (GDF; neprilysin), multiple sclerosis(β-interferon), Parkinson's disease (glial-cell line derivedneurotrophic factor [GDNF]), Huntington's disease (RNAi to removerepeats), Canavan's disease, amyotrophic lateral sclerosis, epilepsy(galanin, neurotrophic factors), and other neurological disorders,cancer (endostatin, angiostatin, TRAIL, FAS-ligand, cytokines includinginterferons; RNAi including RNAi against VEGF or the multiple drugresistance gene product, mir-26a [e.g., for hepatocellular carcinoma]),diabetes mellitus (insulin), muscular dystrophies including Duchenne(dystrophin, mini-dystrophin, insulin-like growth factor I, asarcoglycan [e.g., a, β, γ], RNAi against myostatic myostatinpropeptide, follistatin, activin type II soluble receptor,anti-inflammatory polypeptides such as the Ikappa B dominant mutant,sarcospan, utrophin, mini-utrophin, antisense or RNAi against splicejunctions in the dystrophin gene to induce exon skipping [see, e.g.,WO/2003/095647], antisense against U7 snRNAs to induce exon skipping[see, e.g., WO/2006/021724], and antibodies or antibody fragmentsagainst myostatin or myostatin propeptide) and Becker, Myotonicdystrophy 1 or 2, facioscapulohumeral muscular dystrophy (FSHD), Gaucherdisease (glucocerebrosidase), Hurler's disease (a-L-iduronidase),adenosine deaminase deficiency (adenosine deaminase), glycogen storagediseases (e.g., Fabry disease [a-galactosidase] and Pompe disease[lysosomal acid alpha-glucosidase]) and other metabolic disorders,congenital emphysema (alpha-1-antitrypsin), Lesch-Nyhan Syndrome(hypoxan thine guanine phosphoribosyl transferase), Niemann-Pick disease(sphingomyelinase), Tay-Sachs disease (lysosomal hexosaminidase A),frontotemporal dementia, Maple Syrup Urine Disease (branched-chain ketoacid dehydrogenase), retinal degenerative diseases (and other diseasesof the eye and retina; e.g., PDGF for macular degeneration and/orvasohibin or other inhibitors of VEGF or other angiogenesis inhibitorsto treat/prevent retinal disorders, e.g., in Type I diabetes), diseasesof solid organs such as brain (including Parkinson's Disease [GDNF],astrocytomas [endostatin, angiostatin and/or RNAi against VEGF],glioblastomas [endostatin, angiostatin and/or RNAi against VEGF]),liver, kidney, heart including congestive heart failure or peripheralartery disease (PAD) (e.g., by delivering protein phosphatase inhibitor1 (1-1) and fragments thereof (e.g., IIC), serca2a, zinc finger proteinsthat regulate the phospholamban gene, Barkct, [32-adrenergic receptor,2-adrenergic receptor kinase (BARK), phosphoinositide-3 kinase (PI3kinase), S100A1, parvalbumin, adenylyl cyclase type 6, a molecule thateffects G-protein coupled receptor kinase type 2 knockdown such as atruncated constitutively active bARKct; calsarcin, RNAi againstphospholamban; phospholamban inhibitory or dominant-negative moleculessuch as phospholamban S16E, etc.), arthritis (insulin-like growthfactors), joint disorders (insulin-like growth factor 1 and/or 2),intimal hyperplasia (e.g., by delivering enos, inos), improve survivalof heart transplants (superoxide dismutase), AIDS (soluble CD4), musclewasting (insulin-like growth factor I), kidney deficiency(erythropoietin), anemia (erythropoietin), arthritis (anti-inflammatoryfactors such as I RAP and TNFa soluble receptor), hepatitis(a-interferon), LDL receptor deficiency (LDL receptor), hyperammonemia(ornithine transcarbamylase), Krabbe's disease (galactocerebrosidase),Batten's disease, spinal cerebral ataxias including SCA1, SCA2 and SCA3,phenylketonuria (phenylalanine hydroxylase), autoimmune diseases, andthe like. The compositions and methods disclosed herein can further beused following organ transplantation to increase the success of thetransplant and/or to reduce the negative side effects of organtransplantation or adjunct therapies (e.g., by administeringimmunosuppressant agents or inhibitory nucleic acids to block cytokineproduction). As another example, bone morphogenic proteins (includingBNP 2, 7, etc., RANKL and/or VEGF) can be administered with a boneallograft, for example, following a break or surgical removal in acancer patient.

In some embodiments, the virus vectors described herein can be employedto deliver a heterologous nucleic acid encoding a polypeptide orfunctional RNA to treat and/or prevent a liver disease or disorder. Theliver disease or disorder may be, for example, primary biliarycirrhosis, nonalcoholic fatty liver disease (NAFLD), non-alcoholicsteatohepatitis (NASH), autoimmune hepatitis, hepatitis B, hepatitis C,alcoholic liver disease, fibrosis, jaundice, primary sclerosingcholangitis (PSC), Budd-Chiari syndrome, hemochromatosis, Wilson'sdisease, alcoholic fibrosis, non-alcoholic fibrosis, liver steatosis,Gilbert's syndrome, biliary atresia, alpha-1-antitrypsin deficiency,alagille syndrome, progressive familial intrahepatic cholestasis,Hemophilia B, Hereditary Angioedema (HAE), Homozygous FamilialHypercholesterolemia (HoFH), Heterozygous Familial Hypercholesterolemia(HeFH), Von Gierke's Disease (GSD 1), Hemophilia A, MethylmalonicAcidemia, Propionic Acidemia, Homocystinuria, Phenylketonuria (PKU),Tyrosinemia Type 1, Arginase 1 Deficiency, Argininosuccinate LyaseDeficiency, Carbamoyl-phosphate synthetase 1 deficiency, CitrullinemiaType 1, Citrin Deficiency, Crigler-Najjar Syndrome Type 1, Cystinosis,Fabry Disease, Glycogen Storage Disease 1b, LPL Deficiency,N-Acetylglutamate Synthetase Deficiency, Ornithine TranscarbamylaseDeficiency, Ornithine Translocase Deficiency, Primary Hyperoxaluria Type1, or ADA SCID.

The compositions and methods described herein can also be used toproduce induced pluripotent stem cells (iPS). For example, a virusvector described herein can be used to deliver stem cell associatednucleic acid(s) into a non-pluripotent cell, such as adult fibroblasts,skin cells, liver cells, renal cells, adipose cells, cardiac cells,neural cells, epithelial cells, endothelial cells, and the like.

Nucleic acids encoding factors associated with stem cells are known inthe art. Nonlimiting examples of such factors associated with stem cellsand pluripotency include Oct-3/4, the SOX family (e.g., SOX 1, SOX2,SOX3 and/or SOX 15), the Klf family (e.g., Klfl, KHZ Klf4 and/or Klf5),the Myc family (e.g., C-myc, L-myc and/or N-myc), NANOG and/or LIN28.

The methods described herein can also be practiced to treat and/orprevent a metabolic disorder such as diabetes (e.g., insulin),hemophilia (e.g., Factor IX or Factor VIII), a lysosomal storagedisorder such as a mucopolysaccharidosis disorder (e.g., Sly syndrome[β-glucuronidase], Hurler Syndrome [alpha-L-iduronidase], ScheieSyndrome [alpha-L-iduronidase], Hurler-Scheie Syndrome[alpha-L-iduronidase], Hunter's Syndrome [iduronate sulfatase],Sanfilippo Syndrome A [heparan sulfamidase], B[N-acetylglucosaminidase], C [acetyl-CoA:alpha-glucosaminideacetyltransferase], D [N-acetylglucosamine 6-sulfatase], MorquioSyndrome A [galactoses-sulfate sulfatase], B [3-galactosidase],Maroteaux-Lamy Syndrome [N-acetylgalactosamine-4-sulfatase], etc.),Fabry disease (alpha-galactosidase), Gaucher's disease(glucocerebrosidase), or a glycogen storage disorder (e.g., Pompedisease; lysosomal acid alpha-glucosidase).

Gene transfer has substantial use for understanding and providingtherapy for disease states. There are a number of inherited diseases inwhich defective genes are known and have been cloned. In general, theabove disease states fall into two classes: deficiency states, usuallyof enzymes, which are generally inherited in a recessive manner, andunbalanced states, which may involve regulatory or structural proteins,and which are typically inherited in a dominant manner. For deficiencystate diseases, gene transfer can be used to bring a normal gene intoaffected tissues for replacement therapy, as well as to create animalmodels for the disease using antisense mutations. For unbalanced diseasestates, gene transfer can be used to create a disease state in a modelsystem, which can then be used in efforts to counteract the diseasestate. Thus, virus vectors as described herein permit the treatmentand/or prevention of genetic diseases.

The virus vectors described herein may also be employed to provide afunctional RNA to a cell in vitro or in vivo. The functional RNA may be,for example, a non-coding RNA. In some embodiments, expression of thefunctional RNA in the cell can diminish expression of a particulartarget protein by the cell. Accordingly, functional RNA can beadministered to decrease expression of a particular protein in a subjectin need thereof. In some embodiments, expression of the functional RNAin the cell can increase expression of a particular target protein bythe cell. Accordingly, functional RNA can be administered to increaseexpression of a particular protein in a subject in need thereof. In someembodiments, expression of the functional RNA can regulate splicing of aparticular target RNA in a cell. Accordingly, functional RNA can beadministered to regulate splicing a particular RNA in a subject in needthereof. In some embodiments, expression of the functional RNA in thecell can regulate the function of a particular target protein by thecell. Accordingly, functional RNA can be administered to regulate thefunction of a particular protein in a subject in need thereof.Functional RNA can also be administered to cells in vitro to regulategene expression and/or cell physiology, e.g., to optimize cell or tissueculture systems or in screening methods.

In addition, virus vectors as described herein find use in diagnosticand screening methods, whereby a nucleic acid of interest is transientlyor stably expressed in a cell culture system, or alternatively, atransgenic animal model.

The virus vectors can also be used for various non-therapeutic purposes,including but not limited to use in protocols to assess gene targeting,clearance, transcription, translation, etc., as would be apparent to oneskilled in the art. The virus vectors can also be used for the purposeof evaluating safety (spread, toxicity, immunogenicity, etc.). Suchdata, for example, are considered by the United States Food and DrugAdministration as part of the regulatory approval process prior toevaluation of clinical efficacy.

In some embodiments, the virus vectors may be used to produce an immuneresponse in a subject. According to this embodiment, a virus vectorcomprising a heterologous nucleic acid sequence encoding an immunogenicpolypeptide can be administered to a subject, and an active immuneresponse is mounted by the subject against the immunogenic polypeptide.Immunogenic polypeptides are as described hereinabove. In someembodiments, a protective immune response is elicited.

Alternatively, the virus vector may be administered to a cell ex vivoand the altered cell is administered to the subject. The virus vectorcomprising the heterologous nucleic acid is introduced into the cell,and the cell is administered to the subject, where the heterologousnucleic acid encoding the immunogen can be expressed and induce animmune response in the subject against the immunogen. In someembodiments, the cell is an antigen-presenting cell (e.g., a dendriticcell).

An “active immune response” or “active immunity” is characterized by“participation of host tissues and cells after an encounter with theimmunogen. It involves differentiation and proliferation ofimmunocompetent cells in lymphoreticular tissues, which lead tosynthesis of antibody or the development of cell-mediated reactivity, orboth.” Herbert B. Herscowitz, Immunophysiology: Cell Function andCellular Interactions in Antibody Formation, in IMMUNOLOGY: BASICPROCESSES 117 (Joseph A. Bellanti ed., 1985). Alternatively stated, anactive immune response is mounted by the host after exposure to animmunogen by infection or by vaccination. Active immunity can becontrasted with passive immunity, which is acquired through the transferof preformed substances (antibody, transfer factor, thymic graft,interleukin-2) from an actively immunized host to a non-immune host.

A “protective” immune response or “protective” immunity as used hereinindicates that the immune response confers some benefit to the subjectin that it prevents or reduces the incidence of disease. Alternatively,a protective immune response or protective immunity may be useful in thetreatment and/or prevention of disease, in particular cancer or tumors(e.g., by preventing cancer or tumor formation, by causing regression ofa cancer or tumor and/or by preventing metastasis and/or by preventinggrowth of metastatic nodules). The protective effects may be complete orpartial, as long as the benefits of the treatment outweigh anydisadvantages thereof.

In some embodiments, the virus vector or cell comprising theheterologous nucleic acid can be administered in an immunogenicallyeffective amount, as described below.

In some embodiments, the virus vectors can be administered for cancerimmunotherapy by administration of a virus vector expressing one or morecancer cell antigens (or an immunologically similar molecule) or anyother immunogen that produces an immune response against a cancer cell.To illustrate, an immune response can be produced against a cancer cellantigen in a subject by administering a virus vector comprising aheterologous nucleic acid encoding the cancer cell antigen, for exampleto treat a patient with cancer and/or to prevent cancer from developingin the subject. The virus vector may be administered to a subject invivo or by using ex vivo methods, as described herein.

Alternatively, the cancer antigen can be expressed as part of the capsidprotein subunit, or be otherwise associated with the protein capsid(e.g., as described above).

As another alternative, any other therapeutic nucleic acid (e.g., RNAi)or polypeptide (e.g., cytokine) known in the art can be administered totreat and/or prevent cancer.

As used herein, the term “cancer” encompasses tumor-forming cancers.Likewise, the term “cancerous tissue” encompasses tumors. A “cancer cellantigen” encompasses tumor antigens.

The term “cancer” has its understood meaning in the art, for example, anuncontrolled growth of tissue that has the potential to spread todistant sites of the body (i.e., metastasize). Exemplary cancersinclude, but are not limited to melanoma, adenocarcinoma, thymoma,lymphoma (e.g., non-Hodgkin's lymphoma, Hodgkin's lymphoma), sarcoma,lung cancer, liver cancer, colon cancer, leukemia, uterine cancer,breast cancer, prostate cancer, ovarian cancer, cervical cancer, bladdercancer, kidney cancer, pancreatic cancer, brain cancer and any othercancer or malignant condition now known or later identified. In someembodiments, a method of treating and/or preventing tumor-formingcancers is provided.

The term “tumor” is also understood in the art, for example, as anabnormal mass of undifferentiated cells within a multicellular organism.Tumors can be malignant or benign. In some embodiments, the methodsdisclosed herein are used to prevent and treat malignant tumors.

By the terms “treating cancer,” “treatment of cancer” and equivalentterms it is intended that the severity of the cancer is reduced or atleast partially eliminated and/or the progression of the disease isslowed and/or controlled and/or the disease is stabilized. In someembodiments, these terms indicate that metastasis of the cancer isprevented or reduced or at least partially eliminated and/or that growthof metastatic nodules is prevented or reduced or at least partiallyeliminated.

By the terms “prevention of cancer” or “preventing cancer” andequivalent terms it is intended that the methods at least partiallyeliminate or reduce and/or delay the incidence and/or severity of theonset of cancer. Alternatively stated, the onset of cancer in thesubject may be reduced in likelihood or probability and/or delayed.

In some embodiments, cells may be removed from a subject with cancer andcontacted with a virus vector expressing a cancer cell antigen asdescribed herein. The modified cell is then administered to the subject,whereby an immune response against the cancer cell antigen is elicited.This method can be advantageously employed with immunocompromisedsubjects that cannot mount a sufficient immune response in vivo (i.e.,cannot produce enhancing antibodies in sufficient quantities).

It is known in the art that immune responses may be enhanced byimmunomodulatory cytokines (e.g., alpha-interferon, beta-interferon,gamma-interferon, omega-interferon, tau-interferon, interleukin-1-alpha,interleukin-1β, interleukin-2, interleukin-3, interleukin-4, interleukin5, interleukin-6, interleukin-7, interleukin-8, interleukin-9,interleukin-10, interleukin-11, interleukin-12, interleukin-13,interleukin-14, interleukin-18, B cell Growth factor, CD40 Ligand, tumornecrosis factor-alpha, tumor necrosis factor-β, monocyte chemoattractantprotein-1, granulocyte-macrophage colony stimulating factor, andlymphotoxin). Accordingly, immunomodulatory cytokines (preferably, CTLinductive cytokines) may be administered to a subject in conjunctionwith the virus vector. Cytokines may be administered by any method knownin the art. Exogenous cytokines may be administered to the subject, oralternatively, a nucleic acid encoding a cytokine may be delivered tothe subject using a suitable vector, and the cytokine produced in vivo.

Subjects, Pharmaceutical Formulations, and Modes of Administration

Virus vectors and viral-like particles as described herein find use inboth veterinary and medical applications. Suitable subjects include bothavians and mammals. The term “avian” as used herein includes, but is notlimited to, chickens, ducks, geese, quail, turkeys, pheasant, parrots,parakeets, and the like. The term “mammals” as used herein includes, butis not limited to, humans, non-human primates, bovines, ovines,caprines, equines, felines, canines, lagomorphs, etc. Human subjectsinclude neonates, infants, juveniles, adults and geriatric subjects.

In some embodiments, the subject is “in need” of the methods describedherein.

In some embodiments, a pharmaceutical composition is provided comprisinga virus vector and/or virus-like particle in a pharmaceuticallyacceptable carrier and, optionally, other medicinal agents,pharmaceutical agents, stabilizing agents, buffers, carriers, adjuvants,diluents, etc. For injection, the carrier will typically be a liquid.For other methods of administration, the carrier may be either solid orliquid. For inhalation administration, the carrier will be respirable,and optionally can be in solid or liquid particulate form.

By “pharmaceutically acceptable” it is meant a material that is nottoxic or otherwise undesirable, i.e., the material may be administeredto a subject without causing any undesirable biological effects.

Also provided herein are method of transferring a nucleic acid to a cellin vitro. The virus vector may be introduced into the cells at theappropriate multiplicity of infection according to standard transductionmethods suitable for the particular target cells. Titers of virus vectorto administer can vary, depending upon the target cell type and number,and the particular virus vector, and can be determined by those of skillin the art without undue experimentation. In some embodiments, at leastabout 10³ infectious units, optionally at least about 10⁵ infectiousunits are introduced to the cell.

The cell(s) into which the virus vector is introduced can be of anytype, including but not limited to neural cells (including cells of theperipheral and central nervous systems, in particular, brain cells suchas neurons and oligodendrocytes), lung cells, cells of the eye(including retinal cells, retinal pigment epithelium, and cornealcells), epithelial cells (e.g., gut and respiratory epithelial cells),muscle cells (e.g., skeletal muscle cells, cardiac muscle cells, smoothmuscle cells and/or diaphragm muscle cells), dendritic cells, pancreaticcells (including islet cells), hepatic cells, myocardial cells, bonecells (e.g., bone marrow stem cells), hematopoietic stem cells, spleencells, keratinocytes, fibroblasts, endothelial cells, prostate cells,germ cells, and the like. In some embodiments, the cell can be anyprogenitor cell. As a further possibility, the cell can be a stem cell(e.g., neural stem cell, liver stem cell). As still a furtheralternative, the cell can be a cancer or tumor cell. Moreover, the cellcan be from any species of origin, as indicated above.

The virus vector can be introduced into cells in vitro for the purposeof administering the modified cell to a subject. In some embodiments,the cells have been removed from a subject, the virus vector isintroduced therein, and the cells are then administered back into thesubject. Methods of removing cells from the subject for manipulation exvivo, followed by introduction back into the subject are known in theart (see, e.g., U.S. Pat. No. 5,399,346). Alternatively, the recombinantvirus vector can be introduced into cells from a donor subject, intocultured cells, or into cells from any other suitable source, and thecells are administered to a subject in need thereof (i.e., a “recipient”subject).

Suitable cells for ex vivo nucleic acid delivery are as described above.Dosages of the cells to administer to a subject will vary upon the age,condition and species of the subject, the type of cell, the nucleic acidbeing expressed by the cell, the mode of administration, and the like.Typically, at least about 10² to about 10⁸ cells or at least about 10³to about 10⁶ cells will be administered per dose in a pharmaceuticallyacceptable carrier. In some embodiments, the cells transduced with thevirus vector are administered to the subject in an effective amount incombination with a pharmaceutical carrier.

In some embodiments, the virus vector is introduced into a cell and thecell can be administered to a subject to elicit an immunogenic responseagainst the delivered polypeptide (e.g., expressed as a transgene or inthe protein capsid). Typically, a quantity of cells expressing animmunogenically effective amount of the polypeptide in combination witha pharmaceutically acceptable carrier is administered. An“immunogenically effective amount” is an amount of the expressedpolypeptide that is sufficient to evoke an active immune responseagainst the polypeptide in the subject to which the pharmaceuticalformulation is administered. In some embodiments, the dosage issufficient to produce a protective immune response (as defined above).The degree of protection conferred need not be complete or permanent, aslong as the benefits of administering the immunogenic polypeptideoutweigh any disadvantages thereof.

Thus, in some embodiments, a method of administering a nucleic acid to acell comprises contacting the cell with the virus vector, virus particleand/or composition as described herein.

Also provided herein is a method of administering the virus vector,virus particle and/or virus-like particle as described herein to asubject. In some embodiments, a method of delivering a nucleic acid to asubject comprises administering to the subject a virus particle, virusvector and/or composition as described herein. Administration of thevirus vectors, virus particles and/or viral-like particles to a humansubject or an animal in need thereof can be by any means known in theart. Optionally, the virus vector, virus particle and/or viral-likeparticle is delivered in an effective dose in a pharmaceuticallyacceptable carrier. In some embodiments, an effective amount of thevirus vector, virus particle and/or viral-like particle is delivered.

The virus vectors and/or viral-like particles described herein canfurther be administered to elicit an immunogenic response (e.g., as avaccine). Typically, immunogenic compositions comprise animmunogenically effective amount of virus vector and/or viral-likeparticle in combination with a pharmaceutically acceptable carrier.Optionally, the dosage is sufficient to produce a protective immuneresponse (as defined above). The degree of protection conferred need notbe complete or permanent, as long as the benefits of administering theimmunogenic polypeptide outweigh any disadvantages thereof. Subjects andimmunogens are as described above.

Dosages of the virus vector and/or viral-like particle to beadministered to a subject depend upon the mode of administration, thedisease or condition to be treated and/or prevented, the individualsubject's condition, the particular virus vector or protein capsid, andthe nucleic acid to be delivered, and the like, and can be determined ina routine manner. In some embodiments, the dose of recombinant AAV is aneffective dose. Exemplary effective doses may be, for example, a dose ofat least about 10⁵, about 10⁶, about 10⁷, about 10⁸, about 10⁹, about10¹⁰, about 10¹¹, about 10¹², about 10¹³, about 10¹⁴, about 10¹⁵transducing units, optionally about 10⁸ to about 10¹³ transducing units.In some embodiments, an effective dose of recombinant AAV is a dose inthe range of about 1×10¹¹ to about 1×10¹⁵ vector genomes per kilogrambody weight of the subject. For example, the effective dose may be about1×10¹¹, about 5×10¹¹, about 1×10¹² about 5×10¹², about 1×10¹³, about5×10¹³, about 1×10¹⁴, about 5×10¹⁴, or about 1×10¹⁵ vector genomes perkilogram (vg/kg) body weight of the subject. In some embodiments, thedose of AAV administered may be 2.8×10¹³ vg/kg or 2.9×10¹³ vg/kg. Insome embodiments, the dose may be 2.1×10¹³ vg or 3.0×10¹³ vg.

In some embodiments, more than one administration (e.g., two, three,four or more administrations) may be employed to achieve the desiredlevel of gene expression over a period of various intervals, e.g.,daily, weekly, monthly, yearly, etc.

Exemplary modes of administration include oral, rectal, transmucosal,intranasal, inhalation (e.g., via an aerosol), buccal (e.g.,sublingual), vaginal, intrathecal, intraocular, transdermal, in utero(or in ovo), parenteral (e.g., intravenous, subcutaneous, intradermal,intramuscular [including administration to skeletal, diaphragm and/orcardiac muscle], intradermal, intrapleural, intracerebral, andintraarticular), topical (e.g., to both skin and mucosal surfaces,including airway surfaces, and transdermal administration),intralymphatic, and the like, as well as direct tissue or organinjection (e.g., to liver, skeletal muscle, cardiac muscle, diaphragmmuscle or brain). Administration can also be to a tumor (e.g., in ornear a tumor or a lymph node). The most suitable route in any given casewill depend on the nature and severity of the condition being treatedand/or prevented and on the nature of the particular vector that isbeing used.

Administration to skeletal muscle includes but is not limited toadministration to skeletal muscle in the limbs (e.g., upper arm, lowerarm, upper leg, and/or lower leg), back, neck, head (e.g., tongue),thorax, abdomen, pelvis/perineum, and/or digits. Suitable skeletalmuscles include but are not limited to abductor digiti minimi (in thehand), abductor digiti minimi (in the foot), abductor hallucis, abductorossis metatarsi quinti, abductor pollicis brevis, abductor pollicislongus, adductor brevis, adductor hallucis, adductor longus, adductormagnus, adductor pollicis, anconeus, anterior scalene, articularisgenus, biceps brachii, biceps femoris, brachialis, brachioradialis,buccinator, coracobrachialis, corrugator supercilii, deltoid, depressoranguli oris, depressor labii inferioris, digastric, dorsal interossei(in the hand), dorsal interossei (in the foot), extensor carpi radialisbrevis, extensor carpi radialis longus, extensor carpi ulnaris, extensordigiti minimi, extensor digitorum, extensor digitorum brevis, extensordigitorum longus, extensor hallucis brevis, extensor hallucis longus,extensor indicis, extensor pollicis brevis, extensor pollicis longus,flexor carpi radialis, flexor carpi ulnaris, flexor digiti minimi brevis(in the hand), flexor digiti minimi brevis (in the foot), flexordigitorum brevis, flexor digitorum longus, flexor digitorum profundus,flexor digitorum superficial is, flexor hallucis brevis, flexor hallucislongus, flexor pollicis brevis. flexor pollicis longus, frontalis,gastrocnemius, geniohyoid, gluteus maximus, gluteus medius, gluteusminimus, gracilis, iliocostalis cervicis, iliocostalis lumborum,iliocostalis thoracis, illiacus, inferior gemellus, inferior oblique,inferior rectus, infraspinatus, interspinalis, intertransversi, lateralpterygoid, lateral rectus, latissimus dorsi, levator anguli oris,levator labii superioris, levator labii superioris alaeque nasi, levatorpalpebrae superioris, levator scapulae, long rotators, longissimuscapitis, longissimus cervicis, longissimus thoracis, longus capitis,longus colli, lumbricals (in the hand), lumbricals (in the foot),masseter, medial pterygoid, medial rectus, middle scalene, multifidus,mylohyoid, obliquus capitis inferior, obliquus capitis superior,obturator externus, obturator internus, occipitalis, omohyoid, opponensdigiti minimi, opponens pollicis, orbicularis oculi, orbicularis oris,palmar interossei, palmaris brevis, palmaris longus, pectineus,pectoralis major, pectoralis minor, peroneus brevis, peroneus longus,peroneus tertius, piriformis, plantar interossei, plantaris, platysma,popliteus, posterior scalene, pronator quadratus, pronator teres, psoasmajor, quadratus femoris, quadratus plantae, rectus capitis anterior,rectus capitis lateralis, rectus capitis posterior major, rectus capitisposterior minor, rectus femoris, rhomboid major, rhomboid minor,risorius, sartorius, scalenus minimus, semimembranosus, semispinaliscapitis, semispinalis cervicis, semispinalis thoracis, semitendinosus,serratus anterior, short rotators, soleus, spinalis capitis, spinaliscervicis, spinalis thoracis, splenius capitis, splenius cervicis,sternocleidomastoid, sternohyoid, sternothyroid, stylohyoid, subclavius,subscapularis, superior gemellus, superior oblique, superior rectus,supinator, supraspinatus, temporalis, tensor fascia lata, teres major,teres minor, thoracis, thyrohyoid, tibialis anterior, tibialisposterior, trapezius, triceps brachii, vastus intermedius, vastuslateralis, vastus medialis, zygomaticus major, and zygomaticus minor,and any other suitable skeletal muscle as known in the art.

The virus vector and/or viral-like particle can be delivered to skeletalmuscle by intravenous administration, intra-arterial administration,intraperitoneal administration, limb perfusion, (optionally, isolatedlimb perfusion of a leg and/or arm; see, e.g. Arruda et al., (2005)Blood 105: 3458-3464), and/or direct intramuscular injection. In someembodiments, the virus vector and/or viral-like particle is administeredto a limb (arm and/or leg) of a subject (e.g., a subject with musculardystrophy such as Duchenne muscular dystrophy (DMD) or limb-girdlemuscular dystrophy (LGMD)) by limb perfusion, optionally isolated limbperfusion (e.g., by intravenous or intra-articular administration). Insome embodiments, the virus vectors and/or viral-like particles canadvantageously be administered without employing “hydrodynamic”techniques. Tissue delivery (e.g., to muscle) of prior art vectors isoften enhanced by hydrodynamic techniques (e.g., intravenous/intravenousadministration in a large volume), which increase pressure in thevasculature and facilitate the ability of the vector to cross theendothelial cell barrier. In some embodiments, the viral vectors and/orviral-like particles can be administered in the absence of hydrodynamictechniques such as high volume infusions and/or elevated intravascularpressure (e.g., greater than normal systolic pressure, for example, lessthan or equal to a 5%, 10%, 15%, 20%, 25% increase in intravascularpressure over normal systolic pressure). Such methods may reduce oravoid the side effects associated with hydrodynamic techniques such asedema, nerve damage and/or compartment syndrome. Administration tocardiac muscle includes administration to the left atrium, right atrium,left ventricle, right ventricle and/or septum. The virus vector and/orviral-like particle can be delivered to cardiac muscle by intravenousadministration, intra-arterial administration such as intra-aorticadministration, direct cardiac injection (e.g., into left atrium, rightatrium, left ventricle, right ventricle), and/or coronary arteryperfusion.

Administration to diaphragm muscle can be by any suitable methodincluding intravenous administration, intra-arterial administration,and/or intra-peritoneal administration.

Delivery to a target tissue can also be achieved by delivering a depotcomprising the virus vector and/or viral-like particle. As describedherein, delivery of a “depot” refers to administration of asustained-action formulation that allows slow release and/or gradualdissemination of the virus, so that the virus can act for longer periodsthan is possible with standard injections. In some embodiments, a depotcomprising the virus vector and/or viral-like particle is implanted intoskeletal, cardiac and/or diaphragm muscle tissue or the tissue can becontacted with a film or other matrix comprising the virus vector and/orviral-like particle. Such implantable matrices or substrates aredescribed in U.S. Pat. No. 7,201,898.

In some embodiments, a virus vector and/or viral-like particle accordingis administered to skeletal muscle, diaphragm muscle and/or cardiacmuscle (e.g., to treat and/or prevent muscular dystrophy, heart disease[for example, PAD or congestive heart failure]).

In some embodiments, the compositions and methods described herein areused to treat and/or prevent diseases or disorders of skeletal, cardiacand/or diaphragm muscle. The diseases or disorders of the muscle may be,for example, muscular dystrophy, myopathy, motor neuron disease, andcardiomyopathy. The diseases or disorders of the muscle may be, forexample, dystrophinopathies, Duchenne muscular dystrophy, Beckermuscular dystrophy, myotonic dystrophies (e.g., myotonic dystrophy 1 and2), facioscapulohumeral muscular dystrophy (FDHD), Eimery-Dreifussmuscular dystrophy, limb-girdle disease, facioscapulohumeral musculardystrophy, oculopharyngeal muscular dystrophy, distal musculardystrophy, congenital muscular dystrophy, juvenile macular dystrophy,centronuclear myopathy, central core myopathy, and inclusion bodymyositis.

In some embodiments, a method of treating and/or preventing musculardystrophy in a subject in need thereof is provided, the methodcomprising: administering a treatment or prevention effective amount ofa virus vector to a mammalian subject, wherein the virus vectorcomprises a heterologous nucleic acid encoding dystrophin, amini-dystrophin, a micro-dystrophin, myostatin propeptide, follistatin,activin type II soluble receptor, IGF-1, anti-inflammatory polypeptidessuch as the Ikappa B dominant mutant, sarcospan, utrophin, amicro-dystrophin, laminin-a2, alpha-sarcoglycan, beta-sarcoglycan,gamma-sarcoglycan, delta-sarcoglycan, IGF-1, an antibody or antibodyfragment against myostatin or myostatin propeptide, and/or RNAi againstmyostatin. In some embodiments, the virus vector can be administered toskeletal, diaphragm and/or cardiac muscle as described elsewhere herein.

Alternatively, methods described herein can be practiced to deliver anucleic acid to skeletal, cardiac or diaphragm muscle, which is used asa platform for production of a polypeptide (e.g., an enzyme) orfunctional RNA (e.g., RNAi, micro RNA, antisense RNA) that normallycirculates in the blood or for systemic delivery to other tissues totreat and/or prevent a disorder (e.g., a metabolic disorder, such asdiabetes [e.g., insulin], hemophilia [e.g., Factor IX or Factor VIII], amucopolysaccharide disorder [e.g., Sly syndrome, Hurler Syndrome, ScheieSyndrome, Hurler-Scheie Syndrome, Hunter's Syndrome, Sanfilippo SyndromeA, B, C, D, Morquio Syndrome, Maroteaux-Lamy Syndrome, etc.] or alysosomal storage disorder such as Gaucher's disease[glucocerebrosidase] or Fabry disease [a-galactosidase A] or a glycogenstorage disorder such as Pompe disease [lysosomal acid alphaglucosidase]). Other suitable proteins for treating and/or preventingmetabolic disorders are described herein. The use of muscle as aplatform to express a nucleic acid of interest is described in U.S.Patent publication US 2002/0192189.

In some embodiments, a method of treating and/or preventing a metabolicdisorder in a subject in need thereof comprises administering atreatment or prevention effective amount of a virus vector to skeletalmuscle of a subject, wherein the virus vector comprises a heterologousnucleic acid encoding a polypeptide, wherein the metabolic disorder is aresult of a deficiency and/or defect in the polypeptide. Illustrativemetabolic disorders and heterologous nucleic acids encoding polypeptidesare described herein. Optionally, the polypeptide is secreted (e.g., apolypeptide that is a secreted polypeptide in its native state or thathas been engineered to be secreted, for example, by operable associationwith a secretory signal sequence as is known in the art). Without beinglimited by any particular theory, according to this embodiment,administration to the skeletal muscle can result in secretion of thepolypeptide into the systemic circulation and delivery to targettissue(s). Methods of delivering virus vectors to skeletal muscle isdescribed in more detail herein.

The methods described herein can also be practiced to produce noncodingRNA, such as antisense RNA, RNAi or other functional RNA (e.g., aribozyme) for systemic delivery.

In some embodiments, a method of treating and/or preventing congenitalheart failure or PAD in a subject in need thereof comprisesadministering a treatment or prevention effective amount of a virusvector to a mammalian subject, wherein the virus vector comprises aheterologous nucleic acid encoding, for example, a sarcoplasmicendoreticulum Ca²⁺-ATPase (SERCA2a), an angiogenic factor, phosphataseinhibitor I (I-1) and fragments thereof (e.g., 11C), RNAi againstphospholamban; a phospholamban inhibitory or dominant-negative moleculesuch as phospholamban S16E, a zinc finger protein that regulates thephospholamban gene, beta-2-adrenergic receptor, beta-2-adrenergicreceptor kinase (BARK), PI3 kinase, calsarcan, a β-adrenergic receptorkinase inhibitor (PARKct), inhibitor 1 of protein phosphatase 1 andfragments thereof (e.g., I1 C), S100A1, parvalbumin, adenylyl cyclasetype 6, a molecule that effects G-protein coupled receptor kinase type 2knockdown such as a truncated constitutively active bARKct, Pim-1, PGC-Iα, SOD-1, SOD-2, EC-SOD, kallikrein, HIF, thymosin-p4, mir-1, mir-133,mir-206, mir-208 and/or mir-26a.

Injectables can be prepared in conventional forms, either as liquidsolutions or suspensions, solid forms suitable for solution orsuspension in liquid prior to injection, or as emulsions. Alternatively,one may administer the virus vector and/or viral-like particle in alocal rather than systemic manner, for example, in a depot orsustained-release formulation. Further, the virus vector and/orviral-like particle can be delivered adhered to a surgically implantablematrix (e.g., as described in U.S. Patent Publication No.US-2004-0013645-A1).

The virus vectors and/or virus-like particles disclosed herein can beadministered to the lungs of a subject by any suitable means, optionallyby administering an aerosol suspension of respirable particles comprisedof the virus vectors and/or virus-like particles, which the subjectinhales. The respirable particles can be liquid or solid. Aerosols ofliquid particles comprising the virus vectors and/or virus-likeparticles may be produced by any suitable means, such as with apressure-driven aerosol nebulizer or an ultrasonic nebulizer, as isknown to those of skill in the art. See, e.g., U.S. Pat. No. 4,501,729.Aerosols of solid particles comprising the virus vectors and/orviral-like particles may likewise be produced with any solid particulatemedicament aerosol generator, by techniques known in the pharmaceuticalart.

The virus vectors and virus-like particles can be administered totissues of the CNS (e.g., brain, eye) and may advantageously result inbroader distribution of the virus vector or virus-like particles thanwould be observed in the absence of the compositions and methodsdescribed herein.

In some embodiments, the virus vectors described herein may beadministered to treat diseases of the CNS, including genetic disorders,neurodegenerative disorders, psychiatric disorders and tumors.Illustrative diseases of the CNS include, but are not limited toAdrenomyeloneuropathy (AMN), Alzheimer's disease, Angelman Syndrome,Frontotemporal Dementia, Parkinson's disease, Huntington's disease,Fragile X syndrome, Canavan disease, Leigh's disease, Refsum disease,Tourette syndrome, primary lateral sclerosis, amyotrophic lateralsclerosis, progressive muscular atrophy, Pick's disease, musculardystrophy, multiple sclerosis, myasthenia gravis, Binswanger's disease,trauma due to spinal cord or head injury, Tay Sachs disease (GM2Gangliosidosis), Lesch-Nyhan disease, MC4R Obesity, MetachromaticLeukodystrophy (MLD), MPS I (Hurler/Scheie), MPS IIIA (Sanfilippo A),Niemann Pick C1, Rett Syndrome, Spinal Muscular Atrophy (SMA), AADCDeficiency, Monogenic Amyotropic Lateral Sclerosis (ALS), Alphamannosidosis, Aspartylglucosaminuria, Dravet Syndrome, Giant AxonalNeuropathy, Globoid Cell Leukodystrophy (Krabbe), Glut 1 Deficiency, GM1Gangliosidosis, Infantile Neuronal Ceroid Lipfuscinosis (INCL, Batten),Juvenile Neuronal Ceroid Lipfuscinosis (JNCL, Batten), Late InfantileNeuronal Ceroid Lipfuscinosis (LINCL, Batten), MPS II (Hunter), MPS IIIB(Sanfilippo B), MPS IIIC (Sanfilippo C), MPS IVA (Morquio Syndrome), MPSVI (Maroteaux-Lamy), Peroxisome Biogenesis Disorders (Zellweger SyndromeSpectrum), Sandhoff Disease (GM2 Gangliosidosis), epilepsy, cerebralinfarcts, psychiatric disorders including mood disorders (e.g.,depression, bipolar affective disorder, persistent affective disorder,secondary mood disorder), schizophrenia, drug dependency (e.g.,alcoholism and other substance dependencies), neuroses (e.g., anxiety,obsessional disorder, somatoform disorder, dissociative disorder, grief,post-partum depression), psychosis (e.g., hallucinations and delusions),dementia, paranoia, attention deficit disorder, psychosexual disorders,sleeping disorders, pain disorders, eating or weight disorders (e.g.,obesity, cachexia, anorexia nervosa, and bulemia) and cancers and tumors(e.g., pituitary tumors) of the CNS.

Disorders of the CNS include ophthalmic disorders involving the retina,posterior tract, and optic nerve (e.g., retinitis pigmentosa, diabeticretinopathy and other retinal degenerative diseases, uveitis,age-related macular degeneration, glaucoma).

Most, if not all, ophthalmic diseases and disorders are associated withone or more of three types of indications: (1) angiogenesis, (2)inflammation, and (3) degeneration. The viral vectors described hereincan be employed to deliver anti-angiogenic factors; anti-inflammatoryfactors; factors that retard cell degeneration, promote cell sparing, orpromote cell growth and combinations of the foregoing.

Diabetic retinopathy, for example, is characterized by angiogenesis.Diabetic retinopathy can be treated by delivering one or moreanti-angiogenic factors either intraocularly (e.g., in the vitreous) orperiocularly (e.g., in the sub-Tenon's region). One or more neurotrophicfactors may also be co-delivered, either intraocularly (e.g.,intravitreally) or periocularly.

Uveitis involves inflammation. One or more anti-inflammatory factors canbe administered by intraocular (e.g., vitreous or anterior chamber)administration of a viral vector.

Retinitis pigmentosa, by comparison, is characterized by retinaldegeneration. In some embodiments, retinitis pigmentosa can be treatedby intraocular (e.g., vitreal administration) of a viral vector encodingone or more neurotrophic factors.

Age-related macular degeneration involves both angiogenesis and retinaldegeneration. This disorder can be treated by administering theinventive viral vectors encoding one or more neurotrophic factorsintraocularly (e.g., vitreous) and/or one or more anti-angiogenicfactors intraocularly or periocularly (e.g., in the sub-Tenon's region).

Glaucoma is characterized by increased ocular pressure and loss ofretinal ganglion cells. Treatments for glaucoma include administrationof one or more neuroprotective agents that protect cells fromexcitotoxic damage using the inventive viral vectors. Such agentsinclude N-methyl-D-aspartate (NMDA) antagonists, cytokines, andneurotrophic factors, delivered intraocularly, optionallyintravitreally.

In some embodiments, the compositions and methods described herein maybe used to treat seizures, e.g., to reduce the onset, incidence orseverity of seizures. The efficacy of a therapeutic treatment forseizures can be assessed by behavioral (e.g., shaking, ticks of the eyeor mouth) and/or electrographic means (most seizures have signatureelectrographic abnormalities). Thus, epilepsy, which is marked bymultiple seizures over time, may also be treated.

In some embodiments, a method of treating a subject in need thereofcomprises administering to the subject an AAV vector comprising aprotein capsid comprising capsid protein subunit, wherein the capsidprotein subunit comprises the amino acid sequence of any one of SEQ IDNO: 165-187. In some embodiments, the AAV vector comprises a proteincapsid comprising a capsid protein subunit comprising the amino acidsequence of SEQ ID NO: 175, or a sequence at least 95% identicalthereto. In some embodiments, the AAV vector comprises a protein capsidcomprising a capsid protein subunit comprising the amino acid sequenceof SEQ ID NO: 175, or a sequence at least 95% identical thereto. In someembodiments, the subject has Dravet syndrome. In some embodiments, thesubject has Rett syndrome. In some embodiments, the subject has Angelmansyndrome. In some embodiments, the subject has Niemann-Pick disease. Insome embodiments, the subject has Fragile X syndrome. In someembodiments, the subject has Alzheimer's disease. In some embodiments,the subject has Gaucher's disease. In some embodiments, the subject hasHuntington's disease. In some embodiments, the subject has Parkinson'sdisease. In some embodiments, the subject has Friedrich's ataxia. Insome embodiments, the AAV vector is administered to the subject byintracerebroventricular (ICV) injection. In some embodiments, the AAVvector is administered to the subject by intrathecal (IT) injection. Insome embodiments, the AAV vector is administered to the subject byintravenous (IV) injection.

In some embodiments, a method of treating a subject in need thereofcomprises administering to the subject an AAV vector comprising aprotein capsid comprising a capsid protein subunit, wherein the capsidprotein subunit comprises the amino acid sequence of SEQ ID NO: 175 or180, wherein the subject has Dravet syndrome, Rett syndrome, Angelmansyndrome, Niemann-Pick disease, or Fragile X syndrome, and wherein theAAV vector is administered to the subject by ICV or IT injection.

In some embodiments, a method of treating a subject in need thereofcomprises administering to the subject an AAV vector comprising aprotein capsid comprising a capsid protein subunit, wherein the capsidprotein subunit comprises the amino acid sequence of SEQ ID NO: 175 or180, wherein the subject has Gaucher's disease, Huntington's disease,Parkinson's disease, or Friedrich's ataxia, and wherein the AAV vectoris administered to the subject by ICV or IT injection.

In some embodiments, somatostatin (or an active fragment thereof) isadministered to the brain using a viral vector to treat a pituitarytumor. According to this embodiment, the viral vector encodingsomatostatin (or an active fragment thereof) is administered bymicroinfusion into the pituitary. Likewise, such treatment can be usedto treat acromegaly (abnormal growth hormone secretion from thepituitary). The nucleic acid (e.g., GenBank Accession No. J00306) andamino acid (e.g., GenBank Accession No. P01166; contains processedactive peptides somatostatin-28 and somatostatin-14) sequences ofsomatostatins are known in the art.

In some embodiments, the virus vector can comprise a secretory signal asdescribed in U.S. Pat. No. 7,071,172.

In some embodiments, the virus vector and/or viral-like particle isadministered to the CNS (e.g., to the brain or to the eye). The virusvector and/or viral-like particle may be introduced into the spinalcord, brainstem (medulla oblongata, pons), midbrain (hypothalamus,thalamus, epithalamus, pituitary gland, substantia nigra, pineal gland),cerebellum, telencephalon (corpus striatum, cerebrum including theoccipital, temporal, parietal and frontal lobes, cortex, basal ganglia,hippocampus and portaamygdala), limbic system, neocortex, corpusstriatum, cerebrum, and inferior colliculus. The virus vector and/orviral-like particle may also be administered to different regions of theeye such as the retina, cornea and/or optic nerve.

The virus vector and/or viral-like particle may be delivered into thecerebrospinal fluid (e.g., by lumbar puncture) for more disperseadministration of the vector. The virus vector and/or viral-likeparticle may further be administered intravascularly to the CNS insituations in which the blood-brain barrier has been perturbed (e.g.,brain tumor or cerebral infarct).

The virus vector and/or viral-like particle can be administered to thedesired region(s) of the CNS by any route known in the art, includingbut not limited to, intrathecal, intra-ocular, intracerebral,intraventricular, intravenous (e.g., in the presence of a sugar such asmannitol), intranasal, intra-aural, intra-ocular (e.g., intra-vitreous,sub-retinal, anterior chamber) and peri-ocular (e.g., sub-Tenon'sregion) delivery as well as intramuscular delivery with retrogradedelivery to motor neurons. In some embodiments, the virus vector and/orviral-like particle is administered in a liquid formulation by directinjection (e.g., stereotactic injection) to the desired region orcompartment in the CNS. In some embodiments, the virus vector and/orviral-like particle may be provided by topical application to thedesired region or by intra-nasal administration of an aerosolformulation. Administration to the eye, may be by topical application ofliquid droplets. As a further alternative, the virus vector and/orviral-like particle may be administered as a solid, slow-releaseformulation (see, e.g., U.S. Pat. No. 7,201,898).

In some embodiments, the virus vector can used for retrograde transportto treat and/or prevent diseases and disorders involving motor neurons(e.g., amyotrophic lateral sclerosis (ALS); spinal muscular atrophy(SMA), etc.). For example, the virus vector can be delivered to muscletissue from which it can migrate into neurons.

EXAMPLES

The following examples, which are included herein for illustrationpurposes only, are not intended to be limiting. As used herein, theterms STRD.101 and STRD.102 are used to describe capsid protein subunitsequences, and AAV-STRD.101 and AAV-STRD.102 are used to describe AAVvectors comprising recombinant or modified capsid protein subunitsequences. However, the terms STRD.101 and STRD.102 may be used in somecontexts to describe AAV vectors comprising a protein capsid comprisingthe named capsid protein subunits, as will be apparent to the skilledartisan.

Example 1. Combinatorial Engineering and Selection of Antibody-EvadingAAV Vectors

Antibody evading AAV mutants are prepared according to the followingmethod. The first step involves identification of conformational 3Dantigenic epitopes on the AAV capsid protein capsid surface, for exampleusing cryo-electron microscopy. Selected residues within antigenicmotifs are then subjected to mutagenesis using degenerate primers witheach codon substituted by nucleotides NNK and gene fragments combinedtogether by Gibson assembly and/or multistep PCR. Capsid proteinsubunit-encoding genes containing a degenerate library of mutatedantigenic motifs are cloned into a wild type AAV genome to replace theoriginal Cap encoding DNA sequence, yielding a plasmid library. Plasmidlibraries are then transfected into 293 producer cell lines with anadenoviral helper plasmid to generate AAV capsid protein subunitlibraries, which can then be subjected to selection. Successfulgeneration of AAV libraries is confirmed via DNA sequencing.

In order to select for new AAV strains that can escape neutralizingantibodies (NAbs) and/or target the central nervous system (CNS), AAVlibraries are subjected to multiple rounds of infection in non-humanprimates. At each stage, tissues of interest are isolated from animalsubjects. Cell lysates harvested from the tissues of interest aresequenced to identify AAV isolates escaping antibody neutralization.After multiple rounds of infection in non-human primates, the isolatedsequences from each mutagenized region are combined in all permutationsand combinations.

As a specific example, a common antigenic motif on an AAV capsid proteinsubunit (VP1) was subjected to mutagenesis as described above. Thedegenerate libraries (FIG. 1A) were then subjected to a first round ofinfection in a non-human primate (intravenous injection). Tissues wereharvested at day 7 post-infection and sequenced to identify single AAVisolates.

Various recombinant AAV isolates were identified in tissue samples,including the spinal cord, dorsal root ganglion, frontal lobe, temporallobe, occipital lobe, putamen, globus pallidus, thalamus, amygdala,hippocampus, substantia nigra, pons, cerebellum, medulla. Results fromthis first round of evolution are shown in FIG. 1B.

The recombinant AAVs isolated during the first round of evolution (FIG.1B) were then reintroduced into a second non-human primate. Tissues wereharvested at day 7 post-infection and sequenced to identify single AAVisolates. The results from this second round of evolution are shown inFIG. 1C.

Recombinant AAVs with the highest frequency were sequenced.Substitutions present in these AAVs are shown in Tables 7.1 and 7.2.These data demonstrate that recombinant AAV virions having capsidprotein subunits comprising the substitutions listed in Tables 7.1 and7.2 evade neutralizing antibodies in vivo in non-human primates and havea tropism for the desired target tissues.

Example 2: Manufacturability of Recombinant AAV Vectors

To determine whether various recombinant AAVs identified in Example 1may be manufactured in large-scale systems, the AAVs were producedaccording to standard methods, and yield was compared to that ofwildtype AAV vectors.

AAVs were produced in HEK293 cells according to a standard tripletransfection protocol. Briefly, the cells were transfected with (i) aplasmid comprising either the wildtype AAV9 capsid protein subunitsequence, the STRD.101 capsid protein subunit variant sequence (SEQ IDNO: 180), or the STRD.102 capsid protein subunit variant sequence (SEQID NO: 175), (ii) a plasmid comprising a 5′ITR, a transgene, and a 3′ITR sequence, and (ii) a plasmid comprising helper genes necessary forAAV production. Two different transgenes were used with each capsidprotein subunit, in self-complementary constructs. The cells weresubsequently lysed and the virions were purified using an affinitycolumn, CsCl density ultracentrifugation, and dialysis. Subsequently,yield of each AAV was measured using a PCR-based quantificationapproach.

As shown in FIG. 2 , recombinant AAV vectors comprising the STRD.101 andSTRD.102 capsid protein subunits had a yield that was similar to theyield of wildtype AAV9. This data confirms that recombinant AAVscomprising the recombinant capsid protein subunits are suitable forcommercial manufacturing.

Example 3: In Vitro Transduction Using Recombinant AAV Viral Vectors

To confirm whether the recombinant AAV vectors of Example 1 aregenerally infective and able to transduce cells in culture, various AAVvectors were prepared according to a standard protocol.

The infectivity of the recombinant AAVs was tested using a standardTCID50 assay. Briefly, HeLaRC32 cells were infected with recombinant AAVparticles in the presence of Adenovirus (Ad5) at doses spanning 5 ordersof magnitude. After 72 hours, DNA was extracted and vector genomereplication was quantified by qPCR.

The particle to infectivity ratio was calculated to determineinfectivity. As shown in FIG. 3 , the infectivity ratio of anAAV-STRD.101 vector was lower compared to that of wildtype AAV9. Becausea lower infectivity ratio translates to a higher potency, AAV-STRD.101is more infectious than wildtype AAV9.

Separately, infectivity was also determined in various cell lines.Recombinant AAVs packaging a luciferase transgene were generated andcontacted with the cells in culture at a dose of 10,000 vector genomes(vg) per cell. 48-hours post infection, cells were lysed. The lysate wascontacted with a bioluminescent substrate, and relative fluorescenceunits (RFUs) were measured. As shown in FIG. 4A-4D, AAV-STRD.101 vectorsinfected U87 cells (human glioblastoma cell line, FIG. 4A), N2A cells(mouse neural crest-derived cell line, FIG. 4B), SY5Y cells (humanneuroblastoma cell line, FIG. 4C), and U2OS cells (human osteosarcomacell line, FIG. 4D) at levels comparable to wildtype AAV9.

Accordingly, this data demonstrates that the recombinant AAV vectors ofExample 1 can effectively transduce cells in culture.

Example 4: In Vivo Characterization of Recombinant AAVs Targeting theCentral Nervous System

Recombinant capsid protein subunits STRD.101 and STRD.102 were selectedfor in vivo characterization. Recombinant AAVs comprising these capsidprotein subunits and packaging a native tdTomato fluorescent transgenewere generated. The recombinant AAVs were administered to neonatal miceby intracerebroventricular injection at day 0. At three weekspost-injection, brain tissues were harvested and fixed to evaluate theexpression by visual assessment of the tdTomato fluorescence. FIG. 5provides representative images showing tdTomato expression in coronalvibratome sections after 24 hours post-fixation with 4% PFA. These samesections were also visualized using immunohistochemistry (FIG. 6 ). Asshown in the images of FIG. 5 and FIG. 6 , AAV9, AAV-STRD.102 andAAV-STRD.101 vectors each had different distribution in the braintissues, with the highest transgene expression localized near the siteof injection. Taken together, this data shows that the recombinant AAVstested successfully deliver a transgene to target cells in vivo afterintracerbroventricular injection.

The AAV-STRD.101 and AAV-STRD.102 vectors packaging tdTomato were alsoadministered to four adult mice by intravenous injection at a dose of5.5×10¹³ vg/kg. Three weeks post-injection, liver and heart wereharvested and fixed to evaluate the expression profile by visualassessment of tdTomato fluorescence.

Representative images from one mouse showing TdTomato expression invibratrome liver sections after 24 hours post-fixation with 4% PFA areprovided in FIG. 7 . Notably, the AAV-STRD.102 and AAV-STRD.101 vectorswere detargeted to the liver compared to wildtype AAV9. This desirableproperty was unexpected, as no counter screen in the liver was performedduring evolution.

Representative images from one mouse showing TdTomato expression invibratrome heart sections after 24 hours post-fixation with 4% PFA areprovided in FIG. 8 . Notably, the vectors tested had different tropismfor the heart. Specifically, the AAV-STRD.102 vector was less infectivein heart compared to AAV-STRD.101. Because no heart screen was performedduring evolution, this differential transduction was wholly unexpected.

Taken together, this data indicates that the AAV-STRD.102 andAAV-STRD.101 vectors can be successfully used to target CNS tissues invivo, avoid clearance by the liver, and are powerful tools for genetherapy. Given their different tropisms (i.e., AAV-STRD.101 was moreinfective in the heart than AAV-STRD.102), these vectors will bepowerful tools for targeting gene therapy treatments to specificallydesired tissues.

Example 5: Biodistribution of Recombinant AAVs in Non-Human Primates

Recombinant AAVs were administered to non-human primates, in order todetermine biodistribution. Recombinant AAVs were administered byintravenous (IV) and intracerebrovascular (ICV) injection (FIG. 9 ).AAV-STRD.101 was administered at a dose of 2.9×10¹³ vector genomes perkilogram (vg/kg) by IV injection, and 2.1×10¹³ vg by ICV injection(black dots). AAV-STRD.102 was administered at a dose of 2.8×10¹³ vg/kgby IV injection, and 3.0×10¹³ vg by ICV injection (white dots). After 30days, the animals were sacrificed, and viral load in various CNS tissueswas measured by qPCR.

As shown in FIG. 9 , both AAV-STRD.102 and AAV-STRD.101 infected variousCNS tissues. Additionally, because the AAVs showed high levels oftransduction, this data suggest that these AAVs likely avoidneutralizing antibodies in vivo.

Example 6: Cell Therapy Method for Treating a Subject in Need Thereof

Cells are transduced using an AAV vector ex vivo. For some purposes, thecells may be autologous (i.e., derived from the subject to be treated)or allogenic (i.e., derived from a different subject/donor). Aftertransduction of the cells using an AAV, and after expression of atransgene has been verified, the cells are administered to the subjectusing standard clinical methods.

Cells may be administered to the subject once, or administration may berepeated multiple times. The number of cells administered variesdepending on, for example, the disease or condition to be treated, theseverity of the subject's disease/condition, and the subject's heightand weight.

Example 7: Gene Therapy Method for Treating a Subject in Need Thereof

An AAV vector described herein (e.g., an AAV vector comprising a capsidprotein subunit having the sequence of SEQ ID NO: 175 or 180) isadministered to a subject in need thereof, wherein the subject has adisease or disorder of the CNS. The AAV vector is administered to thesubject once, or administration may be repeated multiple times. Theadministration is by one or more routes, such as intravenous (IV),intracerebroventricular (ICV), or intrathecal (IT) injection. The doseof AAV vector varies depending on, for example, the disease or conditionto be treated, the severity of the subject's disease/condition, and thesubject's height and weight. For example, the dose of AAV administeredto the subject may be 2.8×10¹³ vg/kg or 2.9×10¹³ vg/kg when the AAVvector is administered by IV injection. When the AAV vector isadministered by ICV injection, the dose may be 2.1×10¹³ vg or 3.0×10¹³vg. In some protocols, the AAV vector may be administered to the subjectby both IV and ICV injection.

Example 8: Preparation of a Recombinant AAV Vector in Mammalian Cells

Three plasmids are provided. The first plasmid comprises a transfercassette comprising a transgene (SEQ ID NO: 3002) encoding NPC1 flankedby two ITRs (SEQ ID NO: 3003 and 3004). The first plasmid comprises thesequence of any one of SEQ ID NO: 3014-3019. The second plasmidcomprises sequences encoding the Rep and Cap genes. The third plasmidcomprises various “helper” sequences required for AAV production (E4,E2a, and VA).

The three plasmids are transfected into viral production cells (e.g.,HEK293) using an appropriate transfection reagent (e.g.,Lipofectamine™). After incubation at 37° C. for a predetermined periodof time, AAV particles are collected from the media or the cells arelysed to release the AAV particles. The AAV particles are then purifiedand titered using either quantitative PCR (qPCR) or droplet digital PCR(ddPCR) according to standard methods. The AAV particles may be storedat −80° C. for later use.

Example 9: Preparation of a Recombinant AAV Vector in Insect Cells

A first recombinant baculoviral vector is provided. The firstrecombinant baculoviral vector comprises a transfer cassette sequencecomprising a transgene (SEQ ID NO: 3002) encoding NPC1 flanked by twoITRs (SEQ ID NO: 3003 and 3004). The transfer cassette comprises thesequence of any one of SEQ ID NO: 3014-3019.

Insect cells (e.g., Sf9) are co-infected in suspension culture with thefirst recombinant baculoviral vector and a least one additionalrecombinant baculoviral vector comprising sequences encoding the AAV Repand Cap proteins (e.g., the STRD.101 or STRD.012 capsid proteinsubunit). After incubation at 28° C. for a predetermined period of time,AAV particles are collected from the media or the cells are lysed torelease the AAV particles. The AAV particles are then purified andtitered using either quantitative PCR (qPCR) or droplet digital PCR(ddPCR) according to standard methods. The AAV particles may be storedat −80° C. for later use.

Example 10: In Vitro Potency Assay

To determine whether the AAV transfer cassettes described herein areable to rescue the NPC1 lysosomal phenotype in cultured cells, arecombinant AAV2 vector packaging a hNPC1 transfer cassette (SEQ ID NO:3014) was prepared in HEK293 cells using a triple-transfection protocol(See, e.g., Example 1). The AAV2-hNPC1 vector was then used to transducewildtype U2OS cells (osteosarcoma), and U2OS cells which do not expressNPC1 (NPC^(−/−)) in vitro at a multiplicity of infection (MOI) of either5×10³ (5K) or 10×10³ (10K). Cells were then incubated at 37° C. in a 5%CO₂ atmosphere.

NPC1 cells exhibit a characteristic accumulation of cholesterol inlysosomes, which can be monitored by observing the size and number oflysosomes in a cell. In this assay, lysosomal phenotype was monitored bymeasuring accumulation of a fluorescent organelle dye, LysoTracker®(ThermoFisher Scientific©), in the cells. 72 hours after transductionwith the AAV2-hNPC1 vector, 50 mM of LysoTracker® was added to thecells. After 2 hours, the cells were fixed and LysoTracker® fluorescencewas measured.

Results are shown in FIG. 10A. As expected, wildtype U2OS cells did notshow significant accumulation of LysoTracker® fluorescence in lysosomes,whereas the NPC1^(−/−) cells did. Cells transduced with AAV2-hNPC1 at aMOI of either 5K or 10K had significantly reduced accumulation ofLysoTracker® fluorescence in lysosomes.

In a separate assay, cells transduced with hNPC1 were fixed and stainedusing filipin, a histochemical stain for cholesterol. The filipin stain,derived from Streptomyces filipinensis, was purchased from Polysciences,and was used at a final concentration of 50 μg/mL. The cells werevisualized using a Pico Automated Cell Imaging System (ImageXpress®),and filipin stain was quantified. Results are shown in FIG. 10B. Asexpected, wildtype U2OS cells did not show significant cholesterolaccumulation, whereas the NPC1^(−/−) cells did. Cells transduced withAAV2-hNPC1 at a MOI of either 5K or 10K had significantly reducedcholesterol accumulation.

Taken together, these data show that transduction of cells usingAAV2-hNPC successfully rescued lysosomal phenotype in NPC1-deficientU2OS cells.

Example 11: In Vivo Potency Assay

To determine whether the AAV transfer cassettes described herein areable to rescue the NPC1 phenotype in vivo, a recombinant AAV9 vectorpackaging a hNPC1 transfer cassette (SEQ ID NO: 3014) was prepared inHEK293 cells using a triple-transfection protocol (See, e.g., Example1). Mice deficient for NPC1 (i.e., NPC1^(−/−) mice) were injectedintravenously at a dose of 3.0×10¹⁴ vector genomes per kilogram (vg/kg),by retro-orbital injection, with either saline or with the AAV9-hNPC1vector around the age of 24-28 days. Results are shown in FIG. 11 . Allsaline-treated mice died by the age of about 80 days. However, allAAV9-hNPC1-injected animals survived through the duration of experiment.The AAV9-hNPC1-injected mice were sacrificed around 100 days of age foranalysis.

Mice were also challenged in a balance beam walking test, wherein numberof slips were measured as mice walked across a balance beam. The testwas performed at about 8 weeks (56 days) of age. As shown in FIG. 13 ,wildtype mice did not slip off the balance beam. Although there was nostatistically significant difference in the number of slips betweenNPC1^(−/−) mice treated with AAV9-hNPC1 and saline-treated NPC1^(−/−)mice, the average number of slips observed in the AAV9-hNPC1 group wasless.

Behavioral phenotype score of the mice was also assessed at about 10weeks (70 days) of age. The behavioral phenotype score is a compositescore measuring various disease symptoms, including grooming, gait,kyphosis, ledge test, hindlimb clasp, and tremor. (See Alam et al, SciTransl Med, 2016; Guyenet et al, J Vis Exp, 2010). As shown in FIG. 12 ,NPC1^(−/−) mice treated with AAV9-hNPC1 had a significantly reducedscore as compared to saline-treated NPC1^(−/−) mice.

Taken together, these data demonstrate that AAV9-hNPC1 can at leastpartially rescue the disease phenotype of NPC1 deficient mice.

Example 12: Testing a STRD.101 Vector Packaging a Cassette Encoding NPC1In Vitro and In Vivo

An AAV-STRD.101 vector comprising a nucleic acid comprising a transfercassette encoding human NPC1 (e.g., the transfer cassette of SEQ ID NO:14) is prepared according to the method of Example 8 or 9. This vectoris referred to herein as AAV-STRD.101-hNPC1

To determine whether the AAV-STRD.101 vector is able to rescue the NPC1lysosomal phenotype in cultured cells, the AAV-STRD.101-hNPC1 vector isthen used to transduce wildtype U2OS cells (osteosarcoma), and U2OScells which do not express NPC1 (NPC^(−/−)) in vitro at a multiplicityof infection (MOI) of either 5×10³ (5K) or 10×10³ (10K). Cells are thenincubated at 37° C. in a 5% C02 atmosphere.

NPC1 cells exhibit a characteristic accumulation of cholesterol inlysosomes, which can be monitored by observing the size and number oflysosomes in a cell. Accordingly, lysosomal phenotype is monitored bymeasuring accumulation of a fluorescent organelle dye, LysoTracker®(ThermoFisher Scientific®), in the cells. 72 hours after transductionwith the AAV2-hNPC1 vector, 50 mM of LysoTracker® is added to the cells.After 2 hours, the cells are fixed and LysoTracker® fluorescence ismeasured.

In a separate assay, cells transduced with the AAV-STRD.101-hNPC1 vectorare fixed and stained using filipin, a histochemical stain forcholesterol. The filipin stain, derived from Streptomyces filipinensis,is used at a final concentration of 50 μg/mL. The cells are visualizedusing a Pico Automated Cell Imaging System (ImageXpress©), and filipinstain is quantified.

The AAV-STRD.101-hNPC1 vector is also tested to determine whether it canrescue the NPC1 phenotype in vivo. Mice deficient for NPC1 (i.e.,NPC1^(−/−) mice) are injected intravenously at a dose of 3.0×10¹⁴ vg/kg,by retro-orbital injection, with either saline or with the AAV9-hNPC1vector around the age of 24-28 days. Survival is monitored until atleast 100 days of age.

Mice are also challenged in a balance beam walking test, wherein numberof slips are measured as mice walked across a balance beam. The test isperformed at about 8 weeks (56 days) of age.

Behavioral phenotype score of the mice is also assessed at about 10weeks (70 days) of age. The behavioral phenotype score is a compositescore measuring various disease symptoms, including grooming, gait,kyphosis, ledge test, hindlimb clasp, and tremor. (See Alam et al, SciTransl Med, 2016; Guyenet et al, J Vis Exp, 2010).

The foregoing is illustrative of the present invention, and is not to beconstrued as limiting thereof. The invention is defined by the followingclaims, with equivalents of the claims to be included therein.

NUMBERED EMBODIMENTS

Notwithstanding the appended claims, the disclosure sets forth thefollowing numbered embodiments:

1. An adeno-associated virus (AAV) vector comprising: (i) a proteincapsid comprising a capsid protein subunit comprising the sequence ofSEQ ID NO: 180 or 175; and (ii) a nucleic acid encapsidated by theprotein capsid; wherein the nucleic acid comprises a transfer cassette;wherein the transfer cassette comprises from 5′ to 3′: a 5′ invertedterminal repeat (ITR); a promoter; a transgene sequence which encodesthe NPC1 protein; a polyadenylation signal; and a 3′ ITR.

2. The AAV vector of embodiment 1, wherein at least one of the 5′ ITRand the 3′ ITR is about 110 to about 160 nucleotides in length.

3. The AAV vector of embodiment 1 or 2, wherein the 5′ ITR is the samelength as the 3′ ITR.

4. The AAV vector of embodiment 1 or 2, wherein the 5′ ITR and the 3′ITR have different lengths.

5. The AAV vector of any one of embodiments 1-4, wherein at least one ofthe 5′ ITR and the 3′ ITR is isolated or derived from the genome ofAAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11,AAV12, AAVrh8, AAVrh10, AAVrh32.33, AAVrh74, Avian AAV or Bovine AAV.

6. The AAV vector of embodiment 1, wherein the 5′ ITR comprises thesequence of SEQ ID NO: 3003.

7. The AAV vector of embodiment 1, wherein the 3′ ITR comprises thesequence of SEQ ID NO: 3004.

8. The AAV vector of any one of embodiments 1-7, wherein the promoter isa constitutive promoter.

9. The AAV vector of any one of embodiments 1-7, wherein the promoter isan inducible promoter.

10. The AAV vector of any one of embodiments 1-9, wherein the promoteris a tissue-specific promoter.

11. The AAV vector of any one of embodiments 1-7, wherein the promoteris selected from the group consisting of the CBA promoter, the GUSB240promoter, the GUSB379 promoter, the HSVTK promoter, the CMV promoter,the SV40 early promoter, the SV40 late promoter, the metallothioneinpromoter, the murine mammary tumor virus (MMTV) promoter, the Roussarcoma virus (RSV) promoter, the polyhedrin promoter, the chickenp-actin (CBA) promoter, the EF-1 alpha promoter, the dihydrofolatereductase (DHFR) promoter, and the phosphoglycerol kinase (PGK)promoter.

12. The AAV vector of embodiment 11, wherein the promoter is selectedfrom the group consisting of the CBA promoter, the GUSB240 promoter, theGUSB379 promoter, and the HSVTK promoter.

13. The AAV vector of any one of embodiments 1-7, wherein the promotercomprises a sequence at least 95% or 100% identical to any one of SEQ IDNO: 3005, SEQ ID NO: 3006, SEQ ID NO: 3007, or SEQ ID NO: 3008.

14. The AAV vector of any one of embodiments 1-13, wherein the NPC1protein is the human NPC1 protein.

15. The AAV vector of any one of embodiments 1-13, wherein the NPC1protein has a sequence that is at least 90% identical to the sequence ofthe human NPC1 protein.

16. The AAV vector of embodiment 15, wherein the NPC1 protein has asequence that is at least 95% identical to the sequence of the humanNPC1 protein.

17. The AAV vector of embodiment 16, wherein the NPC1 protein has asequence that is at least 98% identical to the sequence of the humanNPC1 protein.

18. The AAV vector of any one of embodiments 1-13, wherein the NPC1protein comprises the sequence of SEQ ID NO: 3001.

19. The AAV vector of any one of embodiments 1-13, wherein the transgenecomprises the sequence of SEQ ID NO: 3002.

20. The AAV vector of any one of embodiments 1-18, wherein thepolyadenylation signal is selected from simian virus 40 (SV40), rBG,α-globin, β-globin, human collagen, human growth hormone (hGH), polyomavirus, human growth hormone (hGH) and bovine growth hormone (bGH).

21. The AAV vector of embodiment 20, wherein the polyadenylation signalis the SV40 polyadenylation signal.

22. The AAV vector of embodiment 20, wherein the polyadenylation signalis the rBG polyadenylation signal.

23. The AAV vector of any one of embodiments 1-19, wherein thepolyadenylation signal comprises the sequence at least 95% or 100%identical to SEQ ID NO: 3012 or to SEQ ID NO: 3013.

24. The AAV vector of any one of embodiments 1-23, wherein the cassettefurther comprises an enhancer.

25. The AAV vector of embodiment 24, wherein the enhancer is the CMVenhancer.

26. The AAV vector of embodiment 24, wherein the enhancer comprises thesequence of SEQ ID NO: 3009, or a sequence at least 95% identicalthereto.

27. The AAV vector of any one of embodiments 1-26, wherein the cassettefurther comprises an intronic sequence.

28. The AAV vector of embodiment 27, wherein the intronic sequence is achimeric sequence.

29. The AAV vector of embodiment 27, wherein the intronic sequence is ahybrid sequence.

30. The AAV vector of embodiment 27, wherein the intronic sequencecomprises a sequence isolated or derived from SV40.

31. The AAV vector of embodiment 27, wherein the intronic sequencecomprises the sequence of any one of SEQ ID NO: 3010-3011.

32. The AAV vector of embodiment 1, wherein the AAV transfer cassettecomprises the sequence of any one of SEQ ID NO: 3014-3019.

33. An adeno-associated virus (AAV) vector comprising: (i) a proteincapsid comprising a capsid protein subunit comprising the sequence ofSEQ ID NO: 180 or 175, or a sequence comprising about 1 to about 25amino acid mutations relative to SEQ ID NO: 180 or 175; and (ii) atransfer cassette encapsidated by the protein capsid; wherein thetransfer cassette comprises from 5′ to 3′: a 5′ inverted terminal repeat(ITR); a promoter; a transgene sequence which encodes the NPC1 protein;a polyadenylation signal; and a 3′ ITR.

34. A composition comprising the AAV vector of any one of embodiments1-33.

35. The composition of embodiment 34, wherein the composition comprisesa pharmaceutically acceptable carrier or excipient.

36. A method for treating a subject in need thereof comprisingadministering to the subject a therapeutically effective amount of theAAV vector of any one of embodiments 1-33, or the composition of any oneof embodiments 34-35.

37. The method of embodiment 36, wherein the subject has Neimann-PickDisease Type C.

38. The method of embodiment 36 or 37, wherein the subject is a humansubject.

39. An adeno-associated virus (AAV) vector comprising: (i) a proteincapsid comprising a capsid protein subunit comprising the sequence ofSEQ ID NO: 180 or 175; and (ii) a transfer cassette encapsidated by theprotein capsid; wherein the transfer cassette comprises from 5′ to 3′: a5′ inverted terminal repeat (ITR); a promoter; a transgene sequencecomprising the sequence of SEQ ID NO: 3002; a polyadenylation signal;and a 3′ ITR.

40. An adeno-associated virus (AAV) vector comprising: (i) a proteincapsid comprising a capsid protein comprising the sequence of SEQ ID NO:180 or 175; and (ii) a nucleic acid encapsidated by the protein capsid;wherein the nucleic acid comprises a transfer cassette; wherein thetransfer cassette comprises from 5′ to 3′: a 5′ inverted terminal repeat(ITR); a promoter; a transgene sequence which encodes the NPC1 protein,wherein the NPC1 protein comprises the sequence of SEQ ID NO: 3001; apolyadenylation signal; and a 3′ ITR.

41. The AAV vector of any one of embodiments 1-33, 39 and 40, whereinthe AAV vector selectively delivers the transfer cassette to a cell ortissue of the central nervous system.

42. The AAV vector of embodiment 41, wherein the tissue of the centralnervous system is the premotor cortex, the thalamus, the cerebellarcortex, the dentate nucleus, the spinal cord, or the dorsal rootganglion.

43. The AAV vector of any one of embodiments 1-33, 39 and 40, whereinthe AAV vector delivers the transfer cassette to the brain, but does notdeliver the AAV vector to the heart.

44. The AAV vector of any one of embodiments 1-33, 39 and 40, whereinthe AAV vector delivers the transfer cassette to the brain and to theheart.

45. The AAV vector of embodiment 44, wherein delivery of the transfercassette is greater to the brain than to the heart.

46. The AAV vector of embodiment 44, wherein delivery of the transfercassette is approximately equal in the brain in the heart.

47. A cell comprising the AAV vector of any one of embodiments 1-33 and39-46.

48. An in vitro method of introducing a transfer cassette into a cell,comprising contacting the cell with the AAV vector of any one ofembodiments 1-33 and 39-46.

49. An AAV vector of any one of embodiments 1-33 and 39-46 for use as amedicament.

50. An AAV vector of any one of embodiments 1-33 and 39-46 for use in amethod of treating or preventing Neimann-Pick Disease Type C in asubject in need thereof.

51. The AAV vector of any one of embodiments 1-33 and 39-46, wherein thecapsid protein subunit comprises the sequence of SEQ ID NO: 180.

52. The AAV vector of any one of embodiments 1-33 and 39-46, wherein thecapsid protein subunit comprises the sequence of SEQ ID NO: 175.

53. An Adeno-Associated Virus (AAV) transfer cassette comprising, from5′ to 3′: a 5′ inverted terminal repeat (ITR); a promoter; a transgene;a polyadenylation signal; and a 3′ ITR; wherein the transgene encodesthe NPC1 protein.

54. The AAV transfer cassette of embodiment 53, wherein at least one ofthe 5′ ITR and the 3′ ITR is about 110 to about 160 nucleotides inlength.

55. The AAV transfer cassette of embodiment 53 or 54, wherein the 5′ ITRis the same length as the 3′ ITR.

56. The AAV transfer cassette of embodiment 53 or 54, wherein the 5′ ITRand the 3′ ITR have different lengths.

57. The AAV transfer cassette of any one of embodiments 53-56, whereinat least one of the 5′ ITR and the 3′ ITR is isolated or derived fromthe genome of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9,AAV10, AAV11, AAV12, AAVrh8, AAVrh10, AAVrh32.33, AAVrh74, Avian AAV orBovine AAV.

58. The AAV transfer cassette of embodiment 53 wherein the 5′ ITRcomprises the sequence of SEQ ID NO: 3003.

59. The AAV transfer cassette of embodiment 53, wherein the 3′ ITRcomprises the sequence of SEQ ID NO: 3004.

60. The AAV transfer cassette of any one of embodiments 53-59, whereinthe promoter is a constitutive promoter.

61. The AAV transfer cassette of any one of embodiments 53-59, whereinthe promoter is an inducible promoter.

62. The AAV transfer cassette of any one of embodiments 53-59, whereinthe promoter is a tissue-specific promoter.

63. The AAV transfer cassette of any one of embodiments 53-59, whereinthe promoter is selected from the group consisting of the CBA promoter,the GUSB240 promoter, the GUSB379 promoter, the HSVTK promoter, the CMVpromoter, the SV40 early promoter, the SV40 late promoter, themetallothionein promoter, the murine mammary tumor virus (MMTV)promoter, the Rous sarcoma virus (RSV) promoter, the polyhedrinpromoter, the chicken p-actin (CBA) promoter, the EF-1 alpha promoter,the dihydrofolate reductase (DHFR) promoter, and the phosphoglycerolkinase (PGK) promoter.

64. The AAV transfer cassette of embodiment 63, wherein the promoter isselected from the group consisting of the CBA promoter, the GUSB240promoter, the GUSB379 promoter, and the HSVTK promoter.

65. The AAV transfer cassette of any one of embodiments 53-59, whereinthe promoter comprises a sequence at least 95% or 100% identical to anyone of SEQ ID NO: 3005, SEQ ID NO: 3006, SEQ ID NO: 3007, or SEQ ID NO:3008.

66. The AAV transfer cassette of any one of embodiments 53-65, whereinthe NPC1 protein is the human NPC1 protein.

67. The AAV transfer cassette of any one of embodiments 53-65, whereinthe NPC1 protein has a sequence that is at least 90% identical to thesequence of the human NPC1 protein.

68. The AAV transfer cassette of embodiment 67, wherein the NPC1 proteinhas a sequence that is at least 95% identical to the sequence of thehuman NPC1 protein.

69. The AAV transfer cassette of embodiment 68, wherein the NPC1 proteinhas a sequence that is at least 98% identical to the sequence of thehuman NPC1 protein.

70. The AAV transfer cassette of any one of embodiments 53-65, whereinthe NPC1 protein comprises the sequence of SEQ ID NO: 3001.

71. The AAV transfer cassette of any one of embodiments 53-65, whereinthe transgene comprises the sequence of SEQ ID NO: 3002.

72. The AAV transfer cassette of any one of embodiments 53-71, whereinthe polyadenylation signal is selected from simian virus 40 (SV40), rBG,α-globin, β-globin, human collagen, human growth hormone (hGH), polyomavirus, human growth hormone (hGH) and bovine growth hormone (bGH).

73. The AAV transfer cassette of embodiment 72, wherein thepolyadenylation signal is the SV40 polyadenylation signal.

74. The AAV transfer cassette of embodiment 72, wherein thepolyadenylation signal is the rBG polyadenylation signal.

75. The AAV transfer cassette of any one of embodiments 53-71, whereinthe polyadenylation signal comprises the sequence at least 95% or 100%identical to SEQ ID NO: 3012 or to SEQ ID NO: 3013.

76. The AAV transfer cassette of any one of embodiments 53-75, whereinthe cassette further comprises an enhancer.

77. The AAV transfer cassette of embodiment 76, wherein the enhancer isthe CMV enhancer.

78. The AAV transfer cassette of embodiment 76, wherein the enhancercomprises the sequence of SEQ ID NO: 3009, or a sequence at least 95%identical thereto.

79. The AAV transfer cassette of any one of embodiments 53-78, whereinthe cassette further comprises an intronic sequence.

80. The AAV transfer cassette of embodiment 79, wherein the intronicsequence is a chimeric sequence.

81. The AAV transfer cassette of embodiment 79, wherein the intronicsequence is a hybrid sequence.

82. The AAV transfer cassette of embodiment 79, wherein the intronicsequence comprises sequences isolated or derived from SV40.

83. The AAV transfer cassette of embodiment 79, wherein the intronicsequence comprises the sequence of any one of SEQ ID NO: 3010-3011.

84. The AAV transfer cassette of embodiment 53, wherein the AAV transfercassette comprises the sequence of any one of SEQ ID NO: 3014-3019.

85. A plasmid comprising the AAV transfer cassette of any one ofembodiments 53-84.

86. A cell comprising the AAV transfer cassette of any one ofembodiments 53-84 or the plasmid of embodiment 85.

87. A method of producing a recombinant AAV vector, the methodcomprising contacting an AAV producer cell with the AAV transfercassette of any one of embodiments 53-84 or the plasmid of embodiment85.

88. A recombinant AAV vector produced by the method of embodiment 87.

89. The recombinant AAV vector of embodiment 88, wherein the vector isof a serotype selected from AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7,AAV8, AAV9, AAV10, AAV11, AAV12, AAVrh8, AAVrh10, AAVrh32.33, AAVrh74,Avian AAV and Bovine AAV.

90. A composition comprising the AAV transfer cassette of any one ofembodiments 53-84, the plasmid of embodiment 85, the cell of embodiment86, or the recombinant AAV vector of embodiment 88 or 89.

91. A method for treating a subject in need thereof comprisingadministering to the subject an effective amount of the AAV transfercassette of any one of embodiments 53-84, the plasmid of embodiment 85,the cell of embodiment 86, or the recombinant AAV vector of embodiment88 or 89.

92. The method of embodiment 91, wherein the subject suffers from thedisease NPC1.

93. The method of embodiment 91 or 92, wherein the subject is a humansubject.

94. An adeno-associated virus (AAV) vector comprising: (i) a proteincapsid comprising a capsid protein subunit comprising the sequence ofSEQ ID NO: 180; and (ii) a nucleic acid encapsidated by the proteincapsid; wherein the nucleic acid comprises a transfer cassette; whereinthe transfer cassette comprises, from 5′ to 3′: a 5′ inverted terminalrepeat (ITR); a promoter; a transgene that encodes the NPC1 protein; apolyadenylation signal; and a 3′ ITR.

95. An adeno-associated virus (AAV) vector comprising: (i) a proteincapsid comprising a capsid protein subunit comprising the sequence ofSEQ ID NO: 180, or a sequence comprising about 1 to about 25 amino acidmutations relative to SEQ ID NO: 180; and (ii) a nucleic acidencapsidated by the protein capsid; wherein the nucleic acid comprises atransfer cassette; wherein the transfer cassette comprises from 5′ to3′: a 5′ inverted terminal repeat (ITR); a promoter; a transgene whichencodes the NPC1 protein; a polyadenylation signal; and a 3′ ITR.

96. The AAV vector of embodiment 94 of 95, wherein the transfer cassettecomprises an intronic sequence.

97. The AAV vector of any one of embodiments 94-96, wherein the intronicsequence comprises the sequence of SEQ ID NO: 10.

98. The AAV vector of any one of embodiments 94-97, wherein the 5′ ITRcomprises the sequence of SEQ ID NO: 3003.

99. The AAV vector of any one of embodiments 94-98, wherein the 3′ ITRcomprises the sequence of SEQ ID NO: 3004.

100. The AAV vector of any one of embodiments 94-99, wherein thepromoter is the CBA promoter.

101. The AAV vector of any one of embodiments 94-99, wherein thepromoter comprises the sequence of SEQ ID NO: 3005.

102. The AAV vector of any one of embodiments 94-101, wherein the NPC1protein is the human NPC1 protein.

103. The AAV vector of any one of embodiments 94-101, wherein the NPC1protein comprises the sequence of SEQ ID NO: 3001.

104. The AAV vector of any one of embodiments 94-101, wherein thetransgene comprises the sequence of SEQ ID NO: 3002.

105. The AAV vector of any one of embodiments 94-104, wherein thepolyadenylation signal is the SV40 polyadenylation signal.

106. The AAV vector of any one of embodiments 94-104, wherein thepolyadenylation signal comprises the sequence of SEQ ID NO: 3012.

107. The AAV vector of any one of embodiments 94-106, wherein thecassette comprises an enhancer.

108. The AAV vector of embodiment 94, wherein the AAV transfer cassettecomprises the sequence of SEQ ID NO: 3014

109. The AAV vector of embodiment 94, wherein the AAV transfer cassettecomprises the sequence of any one of SEQ ID NO: 3015-3019.

110. A composition comprising the AAV vector of any one of embodiments94-109.

111. A cell comprising the AAV vector of any one of embodiments 94-109.

112. A method for treating a subject in need thereof comprisingadministering to the subject an effective amount of the AAV vector ofany one of embodiments 94-109, the composition of embodiment 110, or thecell of embodiment 111.

113. The method of embodiment 112, wherein the subject has Neimann-PickDisease Type C.

114. The method of embodiment 112 or 113, wherein the subject is a humansubject.

What is claimed is:
 1. An adeno-associated virus (AAV) vectorcomprising: (i) a protein capsid comprising a capsid protein subunitcomprising the sequence of SEQ ID NO: 180; and (ii) a nucleic acidencapsidated by the protein capsid; wherein the nucleic acid comprises atransfer cassette; wherein the transfer cassette comprises, from 5′ to3′: a 5′ inverted terminal repeat (ITR); a promoter; a transgene thatencodes the NPC1 protein; a polyadenylation signal; and a 3′ ITR.
 2. TheAAV vector of claim 1, wherein the transfer cassette comprises anintronic sequence.
 3. The AAV vector of claim 2, wherein the intronicsequence comprises the sequence of SEQ ID NO:
 10. 4. The AAV vector ofclaim 1, wherein the 5′ ITR comprises the sequence of SEQ ID NO: 3003.5. The AAV vector of claim 1, wherein the 3′ ITR comprises the sequenceof SEQ ID NO:
 3004. 6. The AAV vector of claim 1, wherein the promoteris the CBA promoter.
 7. The AAV vector of claim 1, wherein the promotercomprises the sequence of SEQ ID NO:
 3005. 8. The AAV vector of claim 1,wherein the NPC1 protein is the human NPC1 protein.
 9. The AAV vector ofclaim 1, wherein the NPC1 protein comprises the sequence of SEQ ID NO:3001.
 10. The AAV vector of claim 1, wherein the transgene comprises thesequence of SEQ ID NO:
 3002. 11. The AAV vector of claim 1, wherein thepolyadenylation signal is the SV40 polyadenylation signal.
 12. The AAVvector of claim 1, wherein the polyadenylation signal comprises thesequence of SEQ ID NO:
 3012. 13. The AAV vector of claim 1, wherein thecassette comprises an enhancer.
 14. The AAV vector of claim 1, whereinthe AAV transfer cassette comprises the sequence of SEQ ID NO: 3014 15.The AAV vector of claim 1, wherein the AAV transfer cassette comprisesthe sequence of any one of SEQ ID NO: 3015-3019.
 16. An adeno-associatedvirus (AAV) vector comprising: (i) a protein capsid comprising a capsidprotein subunit comprising the sequence of SEQ ID NO: 180, or a sequencecomprising about 1 to about 25 amino acid mutations relative to SEQ IDNO: 180; and (ii) a nucleic acid encapsidated by the protein capsid;wherein the nucleic acid comprises a transfer cassette; wherein thetransfer cassette comprises from 5′ to 3′: a 5′ inverted terminal repeat(ITR); a promoter; a transgene which encodes the NPC1 protein; apolyadenylation signal; and a 3′ ITR.
 17. A composition comprising theAAV vector of any one of claims 1-16.
 18. A cell comprising the AAVvector of any one of claims 1-16.
 19. A method for treating a subject inneed thereof comprising administering to the subject an effective amountof the AAV vector of any one of claims 1-16, the composition of claim17, or the cell of claim
 18. 20. The method of claim 19, wherein thesubject has Neimann-Pick Disease Type C.
 21. The method of claim 19 or20, wherein the subject is a human subject.